Once you have performed a query and returned a list of results, you can either remove individual files from your results listing, or clear the whole listing to start again.
When you remove files from your result list, they do not actually go anywhere - Perceptive Search "hides" file names from the query results, thus reducing the size of the listing with which you have to work. It has no effect on the actual file in the index.
Files can be "hidden" in one of three ways:
The current listing will be removed. Once cleared, it cannot be retrieved; you will need to perform another search.