An apparatus includes a conveyor, a programmable motion device, and a controller. The conveyor preferably includes actuatable rollers, and the programmable motion device is preferably a robotic arm. The controller operates the conveyor, a stopping rail, and a positioning rail to move and position a box in a cutting position relative to the robotic arm. The controller determines three dimension of the box and translates a programmed cut pattern to those determined dimensions. Based on the determined dimensions, the controller then operates the robotic arm to perform the programmed cut pattern in the box with the cutting element. The cutting element preferably has square blade so that each of the four blades can be used to cut a side of the box without having to rotate the cutting element during operation.