I fly with a V.A. that has its own fictional base (scenery)which is not an airport in FS9 and also obviously not contained in the FMC.Is any way possible to fly to and from this base using the FMC.Or how would it be possible to program the FMC after take off from the base airport?

You'll have to add the airport and runways to the airac data files. These are text files with a format that's not too hard to figure out (I did in about an hour but don't have my decode with me at work). As I recall, the only trick was to use spaces instead of tabs. There are separate files for airports and navaids, if you need to add an ILS but this doesn't add the navaid to the MSFS. A third file you may need to add is the SIDSTARS text file if you also have approach, departure or arrival procedures. These are a little more involved but there is an excellent tutorial available to help figure these out. However, if all you're adding is an airport and runway then there is only one text file to edit.