plumbers,carpenters, need some help

My intent was to just remove the sublfloor and replace it, but now I will have to remove both layers. Biggest hassle is cutting round the water supply coming out of the wall and around the flange. my recip saw is at the lake so I am using a circular saw. just wondering how you cut out where the joists are when you use a recip saw. just guessing you lay it down and cut across he top of joist as best you can. With the skill saw I just set the depth. Thanksfor the replies guys. Is the flange glued to the pipe,do I have to cut it off to remove it?