The LensPens are great. But I think they're best used when the lens is not particularly dirty, since they are meant to be used without cleaning fluid. Applying too much pressure to the lens surface in cleaning it, even with a LensPen, runs the risk of leaving cleaning marks. If the lens appears to need significant cleaning, I would recommend using cleaning fluid and a microfiber cloth instead of the LensPen (though the brush on the LensPen is good for removing dust before applying the fluid).
Once the lens has been cleaned with fluid, use the LensPen for touching it up.