diff --git a/ScaFFold/datagen/instance.py b/ScaFFold/datagen/instance.py
index 91067ee..801cb0b 100644
--- a/ScaFFold/datagen/instance.py
+++ b/ScaFFold/datagen/instance.py
@@ -25,7 +25,6 @@
 from pathlib import Path
 
 import numpy as np
-import open3d
 from mpi4py import MPI
 
 from ScaFFold.datagen.generate_fractal_points import generate_fractal_points
@@ -170,33 +169,18 @@ def main(config: Config):
         # Generate points
         points = generate_single_instance(config.point_num, params)
 
-        # Force point_data to be contiguous -- prevents possible segfaults in later Vector3dVector call from non-contiguous arrays
+        # Force point_data to be contiguous
         points_contiguous = np.ascontiguousarray(points, dtype=DEFAULT_NP_DTYPE)
 
-        # Create o3d PointCloud object
-        pointcloud = open3d.geometry.PointCloud()
-
-        # Populate PointCloud points attribute with point_data
-        pointcloud.points = open3d.utility.Vector3dVector(points_contiguous)
-
-        # Construct the long path and short filename
+        # Construct the output path
         out_dir = Path(instance_write_dir) / f"{category:06d}"
-        filename = f"{category:06d}_{instance:04d}.ply"
+        filename = f"{category:06d}_{instance:04d}.npy"
 
         # Ensure parent directory exists
         out_dir.mkdir(parents=True, exist_ok=True)
 
-        # Save current working directory so we can restore it later
-        cwd = os.getcwd()
-        try:
-            # Change to the output directory
-            os.chdir(out_dir)
-
-            # Write with short relative path
-            open3d.io.write_point_cloud(filename, pointcloud)
-        finally:
-            # Always restore the working directory
-            os.chdir(cwd)
+        # Save array to out_dir
+        np.save(out_dir / filename, points_contiguous)
 
     end_time = time.time()
     total_time = end_time - start_time
diff --git a/ScaFFold/datagen/volumegen.py b/ScaFFold/datagen/volumegen.py
index d1120ab..479e67e 100644
--- a/ScaFFold/datagen/volumegen.py
+++ b/ScaFFold/datagen/volumegen.py
@@ -23,7 +23,6 @@
 from typing import Dict
 
 import numpy as np
-import open3d as o3d
 from mpi4py import MPI
 
 from ScaFFold.utils.config_utils import Config
@@ -31,12 +30,11 @@
 DEFAULT_NP_DTYPE = np.float64
 
 
-def load_ply_with_open3d(path: str) -> np.ndarray:
+def load_np_ptcloud(path: str) -> np.ndarray:
     """
-    Read a .ply via Open3D and return an (N,3) array of dtype float64.
+    Read a .npy file and return an (N,3) array of dtype float64.
     """
-    pcd = o3d.io.read_point_cloud(path)
-    pts = np.asarray(pcd.points)
+    pts = np.load(path)
     return pts.astype(DEFAULT_NP_DTYPE, copy=False)
 
 
@@ -204,7 +202,7 @@ def main(config: Dict):
                     "fractals",
                     instances_dir,
                     f"{curr_category:06d}",
-                    f"{curr_category:06d}_{curr_instance:04d}.ply",
+                    f"{curr_category:06d}_{curr_instance:04d}.npy",
                 )
 
                 if not os.path.exists(point_cloud_path):
@@ -213,7 +211,7 @@ def main(config: Dict):
                     )
                     sys.exit(1)
 
-                points = load_ply_with_open3d(point_cloud_path)
+                points = load_np_ptcloud(point_cloud_path)
                 mask3d = points_to_voxelgrid(points, grid_size)
 
                 assert mask3d.shape == volume.shape[:3], (
diff --git a/pyproject.toml b/pyproject.toml
index 1caa3a3..4f8ed54 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,7 +49,6 @@ dependencies = [
   "numba>=0.60.0",
   "tqdm>=4.67.1",
   "wandb>=0.19.6",
-  "open3d>=0.18.0",
   "PyYAML>=6.0.2",
   "distconv @ git+https://github.com/LBANN/DistConv.git@232cba6",
 ]
diff --git a/requirements.txt b/requirements.txt
index 8361868..e0165fb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,7 +5,6 @@ numpy>=1.26.4
 numba>=0.60.0
 tqdm>=4.67.1
 wandb>=0.19.6
-open3d>=0.18.0
 PyYAML>=6.0.2
 mpi4py==4.1.1 --no-binary mpi4py
 distconv @ git+https://github.com/LBANN/DistConv.git@232cba6