I think you could go "Tools" >"Interference Detection", select your model under "Selected Components", clear all in the options except "Make interfering parts transpart", then click "Calculate", you could find all the interfering parts. Modify each of them until no interference shows.
Hope this would help.
and then either remove them or save as a part and merge the bodies together into one
this article is for flow but the same concepts apply to solidworks simulation