Yes and No. The PT-3 was discontinued in 2013 and all of our replacement tour cases and premium soft cases were designed to primarily fit our current line of pedal boards. However, many of our replacement cases will also accommodate discontinued pedal board models. In most of these scenarios, the pedal board may fit in the case with an inch or two of extra space. The cases (PT-32-BTC-X and PT-32-PSC-X) that will accommodate the PT-3 will perfectly fit the 16 inch depth of the board but the inside of the case will have an extra 8 inches of width (the PT-3 is 24 inches wide and the cases are made for 32 inch wide pedal boards).
We suggest using the extra space in the cases for storing cables or other gear. For a tighter fit you can buy some 1" foam from a home improvement store or Amazon and cut it to fit the case. Here's some on Amazon that would work: