Originally Posted by channa
As with everything TSA, that's not consistent. If you get sent to secondary solely (no pun intended

) for shoes, in some locations, they do a secondary only on the shoes. While this may not be procedure, it certainly makes more sense than a full secondary.
I had the full secondary (complete with wallet removal and x-ray) on account of my non-alarming shoes (or refusal to remove them). I even asked the guy "all this because I kept me shoes on?" His reply -- yes.