I'm a bit confused—these folders shouldn't contain the filemaker solution itself, but contain the files from container fields, if the solution has containers configured for external storage.
Therefore, if you have a file called MySoltuion.fmp12 with external storage enabled, RC_Data_FMS will contain a subfolder called MySoltuion, which in turn contains subfolder for each table with container fields, which in turn has subfolders for each container field.
RC_Cache_FMS and RC_StreamingCache_FMS play a similar role for containers holding interactive content such as movies.
I think that if you delete RC_Data_FMS entirely, filemaker server will just recreate it next time you restart the server.
If you're no longer using a particular file, you can use the filemaker sever console to remove a database, and this will also remove the corresponding subfolder from inside RC_Data_FMS.
Alternatively, if you manually deleted the database, it should be OK to delete the corresponding sub-folders (you should use the console to stop the server first, otherwise the folders may be locked). If your are unsure, just move the subfolders to another location, rather than deleting them outright, so that you can put them back again if you realised you've made a mistake.
Hope this helps clarify things.