I imaged some samples and I noticed that as I got close to my substrate (acrylic), the surface began to bubble up. I'm wondering if any one else has seen this before. Could it be that I didn't ground my samples properly and charge was building up near the surface?
This happens often when you increase intensity of the back-scattered electrons signal. You should think about thickness of the film if you need more higher resolution.
It's a very usual thing. To decrease specimen heating you may want to decrease voltage and current.
Since you have TLD detector, I assume you have FE SEM and so you can work at 1-2 kV voltages. Decrease beam current (some call it "spot size") as much as you can, i.e. until nose level becomes too high. Increase scan speed during image acquisition (again, until nose level becomes too high). You can try focusing on a place next to a place of interest, then move specimen and take picture immediately.
In some cases thicker coating can help, but it has significant drawbacks. Long coating times can lead to thermal damage of specimen. In addition thick coating layer can hide fine details you your specimen.
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