diff --git a/README.md b/README.md
index 2004c3d..57068a0 100644
--- a/README.md
+++ b/README.md
@@ -79,9 +79,16 @@ LoD2 CityGML tiles can be converted to GLB per tile while preserving roof/wall s
        -o "work/cityjson/${base}.city.json"
    done
    ```
+   If citygml-tools outputs directories named `<tile>.city.json/`, they contain `<tile>.json` inside.
+   If cjio later reports out-of-range vertex indices during triangulation, clean first:
+   ```bash
+   mkdir -p work/cityjson_clean
+   uv run python scripts/clean_cityjson_vertices.py --input-dir work/cityjson --output-dir work/cityjson_clean
+   ```
 2. Clean + triangulate:
    ```bash
-   for f in work/cityjson/*.city.json; do
+   mkdir -p work/cityjson_tri
+   for f in work/cityjson_clean/*.city.json; do
      base="$(basename "$f" .city.json)"
      input_json="$f/$base.json"  # citygml-tools writes a .json inside the .city.json folder
      uv run cjio --ignore_duplicate_keys "$input_json" upgrade triangulate vertices_clean \
diff --git a/scripts/clean_cityjson_vertices.py b/scripts/clean_cityjson_vertices.py
new file mode 100644
index 0000000..00da2fa
--- /dev/null
+++ b/scripts/clean_cityjson_vertices.py
@@ -0,0 +1,176 @@
+#!/usr/bin/env python3
+"""Drop faces that reference out-of-range vertex indices in CityJSON files."""
+from __future__ import annotations
+
+import argparse
+import json
+import sys
+from pathlib import Path
+from typing import Any, Iterable
+
+
+def parse_args(argv: Iterable[str] | None = None) -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        description="Remove faces referencing invalid vertex indices from CityJSON files."
+    )
+    parser.add_argument(
+        "--input-dir",
+        type=Path,
+        default=Path("work/cityjson"),
+        help="Directory containing CityJSON exports (files or citygml-tools folders).",
+    )
+    parser.add_argument(
+        "--output-dir",
+        type=Path,
+        default=Path("work/cityjson_clean"),
+        help="Directory to write cleaned CityJSON files.",
+    )
+    parser.add_argument(
+        "--pattern",
+        default="**/*.json",
+        help="Glob pattern for input files (defaults to any .json under the input dir).",
+    )
+    return parser.parse_args(argv)
+
+
+def read_json(path: Path) -> dict[str, Any]:
+    with path.open("r", encoding="utf-8") as handle:
+        return json.load(handle)
+
+
+def write_json(path: Path, payload: dict[str, Any]) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    with path.open("w", encoding="utf-8") as handle:
+        json.dump(payload, handle, ensure_ascii=True, indent=2)
+        handle.write("\n")
+
+
+def base_name(path: Path) -> str:
+    name = path.name
+    if name.endswith(".city.json"):
+        return name[: -len(".city.json")]
+    if name.endswith(".json"):
+        return name[: -len(".json")]
+    return path.stem
+
+
+def resolve_input_file(path: Path) -> Path | None:
+    if path.is_file():
+        return path
+    if path.is_dir():
+        candidate = path / f"{path.stem}.json"
+        if candidate.is_file():
+            return candidate
+        matches = list(path.glob("*.json"))
+        if len(matches) == 1:
+            return matches[0]
+    return None
+
+
+def boundary_valid(boundary: Any, vertex_count: int) -> bool:
+    if isinstance(boundary, int):
+        return 0 <= boundary < vertex_count
+    if isinstance(boundary, list):
+        return all(boundary_valid(item, vertex_count) for item in boundary)
+    return False
+
+
+def filter_boundaries(boundaries: list[Any], values: list[Any], vertex_count: int) -> tuple[list[Any], list[Any]]:
+    filtered_boundaries: list[Any] = []
+    filtered_values: list[Any] = []
+
+    for boundary, value in zip(boundaries, values):
+        if isinstance(value, list):
+            nested_boundaries, nested_values = filter_boundaries(boundary, value, vertex_count)
+            if nested_boundaries:
+                filtered_boundaries.append(nested_boundaries)
+                filtered_values.append(nested_values)
+            continue
+
+        if boundary_valid(boundary, vertex_count):
+            filtered_boundaries.append(boundary)
+            filtered_values.append(value)
+
+    return filtered_boundaries, filtered_values
+
+
+def filter_geometry(geometry: dict[str, Any], vertex_count: int) -> dict[str, Any] | None:
+    semantics = geometry.get("semantics")
+    boundaries = geometry.get("boundaries")
+    values = semantics.get("values") if semantics else None
+    if boundaries is None or values is None:
+        return geometry
+
+    filtered_boundaries, filtered_values = filter_boundaries(boundaries, values, vertex_count)
+    if not filtered_boundaries:
+        return None
+
+    filtered_geometry = dict(geometry)
+    filtered_geometry["boundaries"] = filtered_boundaries
+    filtered_geometry["semantics"] = dict(semantics)
+    filtered_geometry["semantics"]["values"] = filtered_values
+    return filtered_geometry
+
+
+def filter_cityobject(cityobject: dict[str, Any], vertex_count: int) -> dict[str, Any] | None:
+    geometries = cityobject.get("geometry") or []
+    filtered_geometries = []
+    for geometry in geometries:
+        filtered_geometry = filter_geometry(geometry, vertex_count)
+        if filtered_geometry:
+            filtered_geometries.append(filtered_geometry)
+
+    if not filtered_geometries:
+        return None
+
+    filtered_object = dict(cityobject)
+    filtered_object["geometry"] = filtered_geometries
+    return filtered_object
+
+
+def clean_cityjson(cityjson: dict[str, Any]) -> dict[str, Any]:
+    vertices = cityjson.get("vertices") or []
+    vertex_count = len(vertices)
+
+    cityobjects = cityjson.get("CityObjects") or {}
+    cleaned_objects = {}
+    for object_id, cityobject in cityobjects.items():
+        cleaned_object = filter_cityobject(cityobject, vertex_count)
+        if cleaned_object:
+            cleaned_objects[object_id] = cleaned_object
+
+    cleaned_cityjson = {k: v for k, v in cityjson.items() if k != "CityObjects"}
+    cleaned_cityjson["CityObjects"] = cleaned_objects
+    return cleaned_cityjson
+
+
+def process_file(path: Path, output_dir: Path) -> int:
+    resolved = resolve_input_file(path)
+    if not resolved:
+        print(f"[skip] cannot resolve CityJSON file for {path}", file=sys.stderr)
+        return 0
+
+    cityjson = read_json(resolved)
+    cleaned = clean_cityjson(cityjson)
+    output_path = output_dir / f"{base_name(path)}.city.json"
+    write_json(output_path, cleaned)
+    return 1
+
+
+def main(argv: Iterable[str] | None = None) -> int:
+    args = parse_args(argv)
+    files = sorted(args.input_dir.glob(args.pattern))
+    if not files:
+        print(f"No input files matched pattern '{args.pattern}' in {args.input_dir}", file=sys.stderr)
+        return 1
+
+    total = 0
+    for path in files:
+        total += process_file(path, args.output_dir)
+
+    print(f"Wrote {total} cleaned file(s) to {args.output_dir}")
+    return 0 if total else 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())