Make sure you know what that pipe is for before cutting it off. 3" cast or steel sounds like a vent line. where does it go after coming out of the floor? If the house is 2 story, it may be the main drain for upstairs fixtures. If you do fill it in, make some sort of a stopper a few inches below the top of the pipe and then fill it in. It may connect to a tee under the flor and just "throwing" some cement into the pipe could clog a connecting pipe.