First. You probably used to much. You only need a lite coat to fill the low spots. Second. like suggested you really want to get the bulk of the material removed in what is called the "green stage". It is were the filler is somewhat hard, but not completely cured. You want to sand with an aggressive grit at this point cause it will want to clog the paper. Some use a "cheese grater" others use coarse grit sand paper.
Once you have it knocked down let it cure the rest of the way about 10-15min then go at it with 80grit and an orbital sander. Proceed to work your way up to finer and finer grit until you reach the desired finish.