How can I replace newer windows that have the flange around the outside of window and attached to house under the siding?

Unless you plan to reside you don't use that window. You are describing a new construction window, you neeed a remodleing window. Ask the folks in the home store to show you the difference.

I'm with Bob, however it depends on what type of siding you have. If you vinyl or aluminum you could temporarily remove the siding and replace the window. It all depends on how bad you want to do it. Siding goes up from the bottom up, it comes down from the top down. If there is not much above the top of the window you may want to just start at the top and work down. If there is a lot of siding, or if you wish, you can start one piece above the window. There is a little tool for unhooking the bottom of one piece from the top of the piece below it. You slip the tool up under the bottom of the top piece, catch the edge that is held in place by the lip on the top of the piece below, pull down and out to separate the two. You then lift the top piece and remove the nails of lower piece. You start at the end of a length of siding, once you get the two pieces started you just pull on the upper piece and they sort of unzip. Works better on vinyl because vinyl is a little more flexible then aluminum.