In SpaceClaim, while the data is still in STL facet form, simply select the facets that are protruding and hit the delete key. That will create a hole in the facet body, but there is a repair tool that will find holes and fill them with new facets.
If you want more information, put the STL file in a .7z or .rar archive and attach it to your reply and say what version of ANSYS you are using.
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