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?