How to accommodate materials deeper than the z-axis?

Not really. I place my project with the carve side down on a table top. I use a 2x4 on each side as a spacer and set the metal bars on top of the 2x4s. This allows me to clamp the bars to the material at an equal height. After the bars are clamped on, I flip it over and set it in the CNC table. From there, I just align by tramming the router back and forth along the x axis.

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