diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 794f34b..eaeff99 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -25,7 +25,7 @@ jobs:
 
       - run: unzip assets/vanilla_structures.zip -d structures
 
-      - run: python __main__.py
+      - run: python cli/__main__.py
       
   test_regolith_filter:
     runs-on: ubuntu-latest
@@ -65,4 +65,4 @@ jobs:
       - name: Compiles
         shell: bash
         working-directory: './regolith-test-project'
-        run: regolith run default
\ No newline at end of file
+        run: regolith run default
diff --git a/__main__.py b/__main__.py
deleted file mode 100644
index efa8227..0000000
--- a/__main__.py
+++ /dev/null
@@ -1,83 +0,0 @@
-from rich.progress import Progress, TextColumn, BarColumn, DownloadColumn, TransferSpeedColumn, TextColumn, TimeRemainingColumn
-import pathlib
-import gzip
-import pynbt
-from time import time
-from java_structures import javaToBedrock
-from os import listdir, makedirs, mkdir
-from os.path import isfile, join, isdir
-import threading
-
-structurePath = 'structures' ## path of structures
-  
-def convert(file):
-  mcstructureFile = file.replace(pathlib.Path(file).suffix, '') + '.mcstructure'
-  print(f"Converting '{file}' to '{mcstructureFile}'")
-
-  print("Reading " + file)
-  io = gzip.open(file, mode="rb+")
-  
-  print("Parsing " + file)
-  startTime = time()
-  nbt = pynbt.NBTFile(io)
-  print(f"Loaded {file} in {round((time() - startTime) * 1000, 2)} ms")
-  
-  mcstructure, size = javaToBedrock(nbt)
-  startTime = time()
-
-  with open(mcstructureFile, 'wb') as io:
-    columns = (
-      TextColumn("[progress.description]{task.description}"),
-      BarColumn(),
-      DownloadColumn(),
-      TransferSpeedColumn(),
-      TextColumn("eta"),
-      TimeRemainingColumn(),
-    )
-    with Progress(*columns, refresh_per_second=30) as progress:
-      task = progress.add_task("[cyan]Writing mcstructure...", total=size)
-      global completed
-      global timer
-      completed = 0
-
-      def write (data: bytes):
-        global completed
-        io.write(data)
-        completed += len(data)
-
-      def renderWriteProgress():
-        global timer
-        progress.update(task, completed=completed)
-        timer = threading.Timer(1 / 30, renderWriteProgress)
-        timer.start()
-
-      renderWriteProgress()
-      mcstructure.save(write, True)
-      
-      # stop progress as mcstructure file has been saved
-      timer.cancel()
-      progress.update(task, completed=completed, total=completed)
-      progress.stop()
-
-      print(f"Wrote {mcstructureFile} in {round((time() - startTime) * 1000, 2)} ms\n")
-
-def get_nbtFiles (dirpath: str) -> list[str]:
-  files = []
-  for f in listdir(dirpath):
-    path = join(dirpath, f)
-    if isfile(path) and f.endswith(".nbt"):
-      files.append(path)
-    elif isdir(path):
-      for file in get_nbtFiles(path):
-        files.append(file)
-  return files
-
-if __name__ == "__main__":  # pragma: no coverage
-  makedirs(structurePath, exist_ok=True)
-  nbtFiles = get_nbtFiles(structurePath)
-
-  if len(nbtFiles) == 0:
-    print(f"There are 0 .nbt files in '{structurePath}' folder.")
-  else:
-    for file in nbtFiles:
-      convert(file=file)
\ No newline at end of file
diff --git a/cli/__main__.py b/cli/__main__.py
new file mode 100644
index 0000000..b5dffa4
--- /dev/null
+++ b/cli/__main__.py
@@ -0,0 +1,124 @@
+from rich.progress import Progress, TextColumn, BarColumn, DownloadColumn, TransferSpeedColumn, TimeRemainingColumn
+import pathlib
+import gzip
+import pynbt
+from time import time
+from java_structures import javaToBedrock
+from os import listdir, makedirs, remove
+from os.path import isfile, join, isdir
+import threading
+import json
+import re
+
+structurePath = 'structures'  # Path of structures
+settings_path = './settings.json'
+
+def get_block_mapping(structure_id: str, settings: dict):
+    for entry in settings.get("block_mapping", []):
+        pattern = entry["structure_id"]
+        if "*" in pattern:
+            regex = re.compile("^" + re.escape(pattern).replace("\\*", ".*") + "$")
+            if regex.match(structure_id):
+                return entry["mapping"]
+        elif pattern == structure_id:
+            return entry["mapping"]
+    return {}
+
+def get_structure_id(file_path: str) -> str:
+    return pathlib.Path(file_path).stem
+
+def convert(file: str, settings: dict):
+    mcstructureFile = file.replace(pathlib.Path(file).suffix, '') + '.mcstructure'
+    structure_id = get_structure_id(file)
+    print(f"Converting '{file}' to '{mcstructureFile}' with structure ID '{structure_id}'")
+
+    print("Reading " + file)
+    io = gzip.open(file, mode="rb+")
+
+    print("Parsing " + file)
+    startTime = time()
+    nbt = pynbt.NBTFile(io)
+    print(f"Loaded {file} in {round((time() - startTime) * 1000, 2)} ms")
+
+    # Get custom mapping
+    block_mapping = get_block_mapping(structure_id, settings)
+
+    mcstructure, size = javaToBedrock(nbt, structure_id, block_mapping)
+    startTime = time()
+
+    with open(mcstructureFile, 'wb') as io:
+        columns = (
+            TextColumn("[progress.description]{task.description}"),
+            BarColumn(),
+            DownloadColumn(),
+            TransferSpeedColumn(),
+            TextColumn("eta"),
+            TimeRemainingColumn(),
+        )
+        with Progress(*columns, refresh_per_second=30) as progress:
+            task = progress.add_task("[cyan]Writing mcstructure...", total=size)
+            global completed
+            global timer
+            completed = 0
+
+            def write(data: bytes):
+                global completed
+                io.write(data)
+                completed += len(data)
+
+            def renderWriteProgress():
+                global timer
+                progress.update(task, completed=completed)
+                timer = threading.Timer(1 / 30, renderWriteProgress)
+                timer.start()
+
+            renderWriteProgress()
+            mcstructure.save(write, True)
+
+            # stop progress as mcstructure file has been saved
+            timer.cancel()
+            progress.update(task, completed=completed, total=completed)
+            progress.stop()
+
+            print(f"Wrote {mcstructureFile} in {round((time() - startTime) * 1000, 2)} ms\n")
+
+def get_nbtFiles(dirpath: str) -> list[str]:
+    files = []
+    for f in listdir(dirpath):
+        path = join(dirpath, f)
+        if isfile(path) and f.endswith(".nbt"):
+            files.append(path)
+        elif isdir(path):
+            for file in get_nbtFiles(path):
+                files.append(file)
+    return files
+
+## -----------
+## MAIN
+## -----------
+def main():
+    # Load settings file
+    if isfile(settings_path):
+        f = open(settings_path, "r")
+        json_file = f.read()
+        settings = json.loads(json_file)
+    else:
+        settings = {}
+    
+    # Convert structures
+    makedirs(structurePath, exist_ok=True)
+    nbtFiles = get_nbtFiles(structurePath)
+    if len(nbtFiles) == 0:
+        print(f"There are 0 .nbt files in '{structurePath}' folder.")
+    else:
+        for file in nbtFiles:
+            convert(file, settings)
+
+        # Delete .nbt files after processing
+        for file in nbtFiles:
+            try:
+                remove(file)
+            except Exception as e:
+                print(f"Error deleting file {file}: {e}")
+
+main()
\ No newline at end of file
diff --git a/java_structures.py b/cli/java_structures.py
similarity index 92%
rename from java_structures.py
rename to cli/java_structures.py
index b607c87..03f1ef0 100644
--- a/java_structures.py
+++ b/cli/java_structures.py
@@ -1,4 +1,5 @@
 from time import time
+import os
 import json, re
 from pynbt import (
     NBTFile,
@@ -12,10 +13,27 @@
 )
 from progress_bar import track
 
-blocksj2b = json.loads(open("./assets/blocksJ2B.json", "r").read())
-bedsj2b = json.loads(open("./assets/bedsJ2B.json", "r").read())
-skullj2b = json.loads(open("./assets/skullJ2B.json", "r").read())
-blockstates = json.loads(open("./assets/blockstates.json", "r").read())
+assets_dir = os.path.abspath('./assets/')
+
+# Construct full paths to your files
+blocksj2b_path = os.path.join(assets_dir, "blocksJ2B.json")
+bedsj2b_path = os.path.join(assets_dir, "bedsJ2B.json")
+skullj2b_path = os.path.join(assets_dir, "skullJ2B.json")
+blockstates_path = os.path.join(assets_dir, "blockstates.json")
+
+# Load JSON files
+with open(blocksj2b_path, "r") as f:
+    blocksj2b = json.load(f)
+
+with open(bedsj2b_path, "r") as f:
+    bedsj2b = json.load(f)
+
+with open(skullj2b_path, "r") as f:
+    skullj2b = json.load(f)
+
+with open(blockstates_path, "r") as f:
+    blockstates = json.load(f)
+
 MC_VERSION = "1.21.0.03"
 
 def checkEntry(blocks, entry):
@@ -106,8 +124,8 @@ def getDynamicBlockIdentifier(blockobject):
 
 def getBlockObject(dynamicblockid: str, format="bedrock"):
     baseidentifier = dynamicblockid.split("[")[0]
-    properties = dynamicblockid.split("[")[1].replace("]", "")
-    if properties.split(",")[0] != "":
+    properties = dynamicblockid.split("[")[1].replace("]", "") if "[" in dynamicblockid else ""
+    if properties:
         properties = properties.split(",")
     else:
         properties = []
@@ -150,7 +168,7 @@ def getBlockObject(dynamicblockid: str, format="bedrock"):
                 print(f"Warning: State name {statename} with value {statevalue} is not a valid state for {baseidentifier}. Valid values: {validValues}.")
         return object
 
-def javaToBedrock(structure: NBTFile):
+def javaToBedrock(structure: NBTFile, structure_id: str, block_mapping: dict):
     blocks: TAG_List = structure["blocks"].value
     palette: TAG_List = structure["palette"].value
     oldsize: TAG_List = structure["size"].value
@@ -191,13 +209,25 @@ def javaToBedrock(structure: NBTFile):
     # applying palette
     startTime = time()
     for i in track(sequence=palette, description="[green]Applying Palette"):
-        # Using prismarine-data, find the java edition ID
         blockId = getDynamicBlockIdentifier(i)
-        if not blockId in blocksj2b:
-            newPalette.append(getBlockObject("minecraft:air[]", "bedrock"))
-        else:
+        baseBlockId = blockId.split("[")[0]  # Get the base block identifier
+
+        # Check for exact match in custom mapping (with brackets)
+        if blockId in block_mapping:
+            mapped_id = block_mapping[blockId]
+            newPalette.append(getBlockObject(mapped_id, "bedrock"))
+        # Check for base identifier match in custom mapping (ignore brackets)
+        elif baseBlockId in block_mapping:
+            mapped_id = block_mapping[baseBlockId]
+            newPalette.append(getBlockObject(mapped_id, "bedrock"))
+        # Fallback to default mapping
+        elif blockId in blocksj2b:
             javaId = blocksj2b[blockId]
             newPalette.append(getBlockObject(javaId, "bedrock"))
+        # Fallback to air if no mapping found
+        else:
+            newPalette.append(getBlockObject("minecraft:air[]", "bedrock"))
+
     if applyWaterloggedBlock:
         newPalette.append(getBlockObject("minecraft:water[liquid_depth=0]", "bedrock"))
     print(f"Finished applying palette in {round((time() - startTime) * 1000, 2)} ms")
diff --git a/progress_bar.py b/cli/progress_bar.py
similarity index 100%
rename from progress_bar.py
rename to cli/progress_bar.py
diff --git a/pynbt.py b/cli/pynbt.py
similarity index 100%
rename from pynbt.py
rename to cli/pynbt.py
diff --git a/nbt-to-mcstructure.spec b/nbt-to-mcstructure.spec
index 7203323..1eab402 100644
--- a/nbt-to-mcstructure.spec
+++ b/nbt-to-mcstructure.spec
@@ -5,7 +5,7 @@ block_cipher = None
 
 
 a = Analysis(
-    ['__main__.py'],
+    ['cli/__main__.py'],
     pathex=[],
     binaries=[],
     datas=[],