Retrofit Window Question

I plan on replacing my 25 year old aluminum windows with some vinyl retrofits. The window guy at the local big box store told me I would get the best fit and a slightly larger window if I cut away the aluminum flanges ( I think that it what it's called) that protrude inward from the frame and install the window directly over the frame. After looking online, I can't find any reference to this being done. Is this a good idea? Thanks.