Use ndstool and apicula to extract model files from an NDS ROM with the original filesystem structure.

extract_nds_models.py

#!/usr/bin/env python3
# Use ndstool to dump the FS off an NDS ROM, then use apicula to recursively
# search all files for models, etc.
import sys, os, subprocess, random, shutil

# !!! IMPORTANT !!!
# Change these to the paths to ndstool and apicula on your system.
NDSTOOL_CMD = 'ndstool'
APICULA_CMD = 'apicula'

def main(rom_path, out_dir):
    if os.path.exists(out_dir):
        raise Exception('Output directory already exists!')

    # Dir for ndstool to extract data files to
    data_dir = os.path.join(out_dir, 'tmp.d.' + hex(random.getrandbits(96))[2:])
    # Temp dir for apicula to put extracted files in
    extract_dir = os.path.join(out_dir, 'tmp.x.' + hex(random.getrandbits(96))[2:])

    def extract(path):
        try:
            rm(extract_dir)
            subprocess.run(
                [APICULA_CMD, 'x', os.path.join(data_dir, path), '-o', extract_dir],
                check=True,
            )
            if not os.path.isdir(extract_dir):
                return
            files = os.listdir(extract_dir)
            if not files:
                return
            if len(files) == 1:
                # If one file is extracted, use the original filename plus the
                # extension of the extracted file
                extension = files[0][files[0].rfind('.')+1:]
                out_path = os.path.join(out_dir, path + '.' + extension)
                os.makedirs(os.path.dirname(out_path), exist_ok=True)
                shutil.move(os.path.join(extract_dir, files[0]), out_path)
            else:
                shutil.move(extract_dir, os.path.join(out_dir, path + '.d'))
        except Exception as e:
            print(f'error extracting {path}: {e}')

    try:
        os.makedirs(out_dir, exist_ok=True)

        subprocess.run(
            [NDSTOOL_CMD, '-x', rom_path, '-d', data_dir],
            check=True,
        )

        for dirpath, __dirnames, filenames in os.walk(data_dir):
            for filename in filenames:
                path = os.path.join(dirpath, filename)
                relpath = os.path.relpath(path, data_dir)
                extract(relpath)
    finally:
        rm(data_dir)
        rm(extract_dir)

def rm(path):
    try:
        shutil.rmtree(path)
    except Exception:
        pass

if len(sys.argv) != 3:
    print('Usage: extract_nds_models.py PATH_TO_ROM OUTPUT_DIR')
else:
    main(sys.argv[1], sys.argv[2])