Hi krass - for planar faces, select the faces and run Edit > Separate on them to break the chunk of them off from the main object. Then run Edit > Separate again to break them into totally individual surfaces. Then run Boolean Union - the booleans will do some processing to merge adjacent planar faces into large planes and will merge the faces together. Then select all the pieces and run Edit > Join to glue them back together.

At some point in the future I would like to update the Merge command to work on faces as well, but one reason why I have not done that as of yet is I have some idea that maybe the regular Join command should do the job of both joining and merging but I have not figured out the details on that yet.

- Michael