If the parting surface between two molds is planar you do not have to go the Boolean way but use PlaneCut instead:
- Make your scan watertight either using ANALYSIS/Inspector (keeps the original surface as it is) or EDIT/MakeSolid (remeshes your surface according to the set parameters)
- Go to SELECT and SelectAll
- All selected run Edit/FlipNormals (this makes it a "negative" surface)
- Construct a cuboid shape (= mold material) including your object totally as a separate object.
- Activate both objects (hold down SHIFT while activating the second object) and run EDIT/Combine.
- Use EDIT/PlaneCut on this result and move the cutting plane to the desired position. If you set CutType to Slice(KeepBoth) you can construct two halves in one go. Run EDIT/Separate in this case to get the two halves as separate objects.
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If the parting surface isn't planar you've to use BooleanDifference (of course this works also if it is planar):
- Construct an object describing one half of the mold.
- Activate this object first and (holding down Shift) your scan as the second object (order important for you want to subtract the shape from the holding material) and run EDIT/BooleanDifference.
Note: If there's a bigger difference of mesh density (e.g. the stock object owns only a few triangles while you scan is made of many tris) you should try to get a similar density at the mold object before doing the boolean (simple way is to run MakeSolid on it)