Grinding the tops off of your clips could weaken your floor considerably.
Builders who use clips on the floors usualy intend to use carpet and don't have to deal with your situation.
If you want to notch out small recesses in an underlayment, or thin plywood, a cheap router like the Black and Decker sold at Wal-Mart will speed you up considerably. Buy a good carbide bit, 1/2" straight cut with a 1/4"shank at Lowe's or The Depot, Skil has inexpensive carbide bits at Lowe's.. Just set the depth on the router to less than the thickness of the underlayment, mark your clip locations and make your cuts. It will still take time, but less than a chisel and knife. A little patience and time invested will give you a much better floor than a quick fix.
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