There are several options... if you window-modded your case you may have some matching ali left to make a square panel and suspend behind the hole with double-sided tape... or you could cut a square of perforated ali sheet instead...
Personally, I prefer the proper approach. Take the removeable caddy, masking tape around the inner front lip, measure in 12mm (0.5") and draw a line all the way round...
Take your dremel, and cut!
And voila!!
Rad mounted, front blanking plates still attached!
This now leaves you with all 4x 5.25" bays free, for any combination of HDDs (in 5.25" adapters) and CD devices (eg: 2x CD / DVD Drives, 2x HDDs in 3.5 > 5.25 adapters, a Matrix Orbital in front of one HDD, a FanBus in front of the other HDD...
Or, alternately, recycle the bits you have left... the part that you sliced off the removeable HDD cage can be remounted into the bsae of the case with 4x screws, to give you back 3x 3.5" HDD Bays conveniently positioned in an airflow path...
Done n' dusted!