How do I clean up a scanned or downloaded 3D model that has spikes, pits, a rough surface, or a thick base?

Work in this order

Fix the big problems at import, trim the base next, smooth the whole surface lightly, and only then touch up single spots. Local sculpting done before a global smooth just gets blurred.

Steps

1. At import, check orientation and undercuts. In the positioning form, check Highlight Undercuts. Dark purple areas will lose detail, and large purple patches on the top surface can also mean the mesh has faces turned inside out. That has to be repaired in the program that made the file.
2. Cut the base off at import. Move the Zero Plane Position In Model slider up until the slab is below the plane, with Discard data below zero plane checked. Uncheck that option only for a dished or recessed model that needs its data below the plane.
3. If the model is already in the job, use Replace Below. Select the component, drag the blue pin in the 3D View to the cut height (or type Replace Value Below), choose Transparent or Plane, and check Lower Component by Value to drop the model by the same amount.
4. Make a safety copy of the component before any smoothing or sculpting.
5. Smooth Components. The slider starts at 50%. Keep Preserve Transparency checked so the silhouette is not blurred into the background. Use the least smoothing that removes the roughness. If the maximum is not enough, click Bake Current Smoothing and smooth again.
6. Remove spikes with Sculpting: choose Smooth, set Mode to Lower, and brush over them. Lower mode keeps the lowest points and only removes material. The official documentation names it for spikes in scanned data.
7. Fill pits and holes the same way with Mode set to Raise.
8. Tidy stray bits on the edge by holding Shift with the Undo Brush, which erases what is under the cursor.

Pro tips

• If the model sits at a slant, fix it at the source: right-click the component, choose reimport, and turn the model with the rotation handles in the import form. Re-import only works if the component has not been changed much, so do it before cleanup.
• Tile the 2D and 3D views while smoothing so you can watch the effect.
• For lowering a very tall model without losing surface detail, see the entry on the Emboss Component tool.