From CT Scan to 3D Print: A DICOM to STL Guide

What DICOM and STL are

DICOM is the standard format for medical images. A CT or MRI study is a stack of 2D slices, each recording tissue density or signal at a given position. STL is the standard format for 3D printing: a surface made of triangles. Converting one to the other means deciding which pixels belong to the structure you want, then building a surface around them.

Step 1: Get a suitable scan

Model quality depends on scan quality. Thin slices (around 1 mm or less) give smoother, more accurate models. Motion artifacts and metal implants create noise that must be cleaned up later. Always anonymize patient data before sharing files outside the hospital system.

Step 2: Segmentation

Segmentation is the process of selecting the anatomy you want to print. Free, open-source tools such as 3D Slicer and InVesalius are widely used for this, and commercial medical segmentation software is available for clinical programs.

• Thresholding: select pixels within a density range. Bone is easy to isolate on CT because it is much denser than soft tissue.
• Region growing and island tools: keep only the connected structure you need and remove the scanner table and other objects.
• Manual editing: paint or erase slice by slice where automatic tools miss thin or low-contrast areas.
• Separate segments: split structures (for example, a tumor and the surrounding bone) so they can be printed in different colors.

Step 3: Export and clean the mesh

Export each segment as an STL. Then open it in a mesh tool (for example Meshmixer, Blender or the repair tools built into many slicers) to fill holes, remove small floating pieces, smooth stair-step artifacts and reduce the triangle count if the file is very large. Keep smoothing light so you do not change clinically relevant anatomy.

Step 4: Slice and print

• Scale: make sure the model is at 1:1 in millimeters. DICOM exports can sometimes come out in the wrong units.
• Orientation: place the model to minimize supports on important surfaces.
• Material: PLA on FDM for bone; clear or colored resin for small, detailed or transparent models.
• Supports: use tree or organic supports where possible; they are easier to remove from complex anatomy.
• Check: compare key dimensions of the print to the scan before the model is used for planning.

Build the skill in-house

Many hospitals begin with a biomedical engineer or a resident who learns segmentation, and one or two printers. Jordan Automation can supply the printers, materials and spare parts in Amman and help your team get the printing side running.

Frequently asked questions