So I did a scan with Clrmamepro and this is how I have it setup.

This is the info that came up for the 50 games I have.
Missing Sets: 6768 of 6996
Wrong SetName Case: 0 [0 fixed]
Wrong Named Sets: 0 [0 fixed]
Missing Roms: 94414 of 97657
Missing Bytes: 49gb of 54gb
Missing BIOS Roms: 97 of 107
Wrong Named Roms: 0 [40 fixed]
Wrong RomName Case: 0 [0 fixed]
Wrong Sized Roms: 2 [0 fixed]
Wrong Date/Time Roms: 0 [0 fixed]
Wrong CRC32s: 0
Wrong MD5s: <n/a>
Wrong SHA1s: <n/a>
Missing Samples: <n/a>
Wrong SampleName Case: <n/a>
Missing CHDs: 219 of 219
Wrong CHD Case: 0 [0 fixed]
Wrong Named CHDs: 0 [0 fixed]
Wrong CHD_MD5/SHA1s: 0
Unneeded Files/Folders: 0 [186 fixed]
Corrupt Containers: 0
Number Of Sets: 6996
Number Of BIOS sets: 35
Number Of Parents: 1525
Number Of Clones: 3213
Number Of Others: 2258
Number Of Roms: 97657
Number Of BIOS Roms: 107
Number Of Samples: 2139
Number Of 'nodump' ROMs: 1100
Number Of 'baddump' ROMs: 510
So you mentioned I need to look for the missing files, whats the point of the rebuilder then?