Plexiglass flush with MDF

Set up a plunge router with about a 3/8" straight cut bit.  Set the plunge depth to the thickness of the plexi..in this case where it's just a cover for the amp, 1/8" thickness will do.  Set up a straight edge guide to run the router against to get a straight mortise cut along the edges of the cutout.  If you're going to carpet the MDF, do a test to find out how deep to set the router.  The thicker gray line in the pic shows where the carpet would terminate.  Set the plexi in the cutout with clear acrylic caulk.  Don't panic when you see the caulk come out white, it cures to clear.  Or of course you could just set the plexi in without any glue at all unless you need it.

Make sure you're not completely enclosing that amplifier.  It needs airflow.