My touch screen is not working properly. It is not synced properly with my Stylus taps, I recalibrated it many times. I even went to game notes to test it afterwards and it will not calibrate.

Is there something stuck in the corners of the screen? Sometimes the screen can mess up if something else comes into contact with the screen at the same time as the stylus.

I did and there is nothing on the screen, is the screen itself broken? I have screen protector on it should I take that off then? I have had my 3DS for almost a year and I have only recently had problems with it.

try taking the screen protector off and see if there's anything that was underneath it... sometimes if the edges are loose, little bits of crud or dust can find their way underneath. if your touchscreen operates normally or calibrates ok without the screen protector on it, you just need a new protector is all.

ooh make sure there are no dents in the screen

Use a very soft brissled tooth brush to clean the invisible gunk from under the edge of the screen. That has worked with my son's grimey 3DS. Dry. Don't get the brush wet.