Toilet flange too high

As you can see the toilet flange is too high, I am remodeling my bathroom and want the flange lower, if you notice in the pictures, there is some sort of soft stuff between the flange/closet and the pipe going down. The stuff on top of the flange is hard. Is there any way I could remove this and put in another closet/toilet flange that I could lower.

It is often possible to lower the flange. It may or may not be easy...depends on what the parts are made of...cast iron/lead/plastic/etc. and how they were put together, as to whether there is any wiggle room.

You need a new flange, which should not be set until the floor is done. Drill & pull the lead out and the flange will come off. Get a new flange and lead it back in on top of the finished floor, then cut the excess pipe off the top.

That flange is pretty well shot anyway. Leading a new flange is the right way to go, but that is a job for a plumber. It won't take him long.