If I were a gambling person I would wager that pen mills alone are responsible for a high percentage of blanks being tossed in the trash.
In my opinion, end mills are fine tools and have their uses in woodworking but unfortunately squaring pen blanks isn't their strong suit!
Rod, several people make and sell small sanding arbors that fit in a drill motor or you could easily make one yourself. This is what I would recommend using for the final squaring.
To give you an idea, visit this article in the library
http://content.penturners.org/articles/2010/turningbetweencenters.pdf
In the top of the first photo you will see a block of wood with a bunch of delrin bushings and an arbor to the right of them. I make these bushings for each kit I make so the blank stays nice and centered on the arbor giving a nice 90 degree trim.
In step #8 you will see a close up of the arbor in use and step #9 shows the results. I tried several types of mills including the six bladed cutters and continued catching edges especially since I use a lot of burls and softer woods so ended up sanding.
The sad thing is that in a previous group buy I went crazy and stocked up on cutters and now have a dozen or so that I'll probably never use! :frown: