You would have to know the position and length of the data you want to remove. Just load in the bytes until you hit the beginning position of the data you want to remove, then seek to the position + the length and continue reading data in. The data you loaded will be the data without the part you don't want, so just save it over the original.
EDIT: Actually instead of reading individual bytes, you could use stream.ReadBytes and use the beginning position as the size, then skip over the part you don't want, then calculate how much data is left after the end of the part you just cut out and read it in too.
EDIT: Actually instead of reading individual bytes, you could use stream.ReadBytes and use the beginning position as the size, then skip over the part you don't want, then calculate how much data is left after the end of the part you just cut out and read it in too.