There are two types of scanners in place:

Rapid Scan which uses backscatter x-ray - http://www.rapiscansystems.com/sec1000.html

L3 ProVision Scanner which uses millimeter (radio) waves - http://www.sds.l-3com.com/products/mmwave.htm

AS for the shoes - TSA makes you take them off because they can (Note military are not require to take their shoes off unless the WTMD alarms).