Will using a screen protector affect my 3ds xl touch screen?

I am looking for a way to keep my 3DS XL screen clean.

I looked up this website: http://en-americas-support.nintendo.com/app/answers/detail/a_id/47/~/how-to-clean-the-screen

But I still can't remove the smudges and tap points caused by my stylus.

Can I use a screen protector without affecting the performance of the stylus?

I use a screen protector and it works just fine. I found this thread which discusses some pros and cons of using a screen protector on a DS. The main caution seems to be keeping them out of the sun for extended periods of time, as they risk bubbling and becoming more of a nuisance than they're designed to be.

However I've used a HORI Screen protector on my 3DS XL for a few weeks now and even when leaving it in the sun (ie playing outside) I haven't seen any problems.

3DS uses resistive touch screens, those screens are mostly not affected by screen protectors, as they rely on pressure.