As far as I know, in RSE this isn't possible directly, our filters only allow SHOWING files with certain patterns (well you could list all patterns that you do want to show).
If your remote server is "nearby" with a fast connection, you could set up an Eclipse Project with a Linked Resource pointing into an RSE filesystem (EFS). Eclipse 3.6 and later support very powerful resource filters that allow both the positive and the negative form, ie you can hide certain files using the Core Resources filters. Just select Project Properties / Resource Filters.