Hugo,
The Raster Catalog To Raster Dataset tool has a parameter called, "Expression", which allows you to select specific records in the catalog to mosaic together.
Since you have RPF catalogs I assume you have the Military Analyst extension installed. There is a mosaic command on the MA toolbar to mosaic subsets of the MA catalog.
If you are using ArcGIS 10, the Mosaic Dataset might be your best option. The RPF tiles will be treated as a mosaic, and unlike a raster catalog, the mosaic dataset can be input into geoprocessing tools. In this case it seems all you would need to do is run the Clip tool on the input mosaic dataset.
Regards,
Eric