erotavlas wrote:
i tried that and the same thing happens, the source looks like its including all the disks in my system which I do not want.
...
I DO NOT want to migrate over the unallocated portion of the disk. How do I do this?
RTFM! 
"Exclude a Source Volume from the Conversion Process" on page 51 of VMware vCenter Converter Standalone 5.0 User's Guide.