Hi Marv,
Having been a Jeweller & using other peoples STL's to mill waxes from, I've been in a similar situation to you...
...my easiest solution was to use 3D-Coat.
Bring your STL into 3DC as a voxel, modify as needed then export as an STL...
...you even have the option to reduce the STL should the modified file be too large for its intended application.
You also have the added benefit with 3DC that voxels can be used with Boolean functions...
...handy for those situations where the STL needs to have something removed from it.
If you're needing to also do renders as part of the modified STL, then 3DC can output OBJ's for that purpose too.
(not something I've done myself, but the features are all there & tutorials abound if I really needed it)
HTH, Colin
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