Here's some suggestions (no specific order):
1. Try using different output settings in COMSOL during STEP export and see if you can get a usable file. If possible please make it output the STEP file as a realistic model (with proper thickness) and then ACE can extract the STEP file and generate the layers you require. https://support.numericalinnovations.com/support/discussions/topics/14000012255 (you will see a sample STEP image with thickness for the metal areas). https://support.numericalinnovations.com/support/discussions/topics/14000003391
Note: The thickness is "relative" and really doesn't matter. When ACE converts a 3D model to 2D, it needs to detect different Z values so it can "create a perpendicular slice" though the 3D model and extract each of the necessary layers you require to fabricate a PCB.
2. Try exporting each layer separately as an individual STEP file. Then you can just convert each STEP file one at a time to gerber (thickness won't matter for just a single layer).
3. ACE can also import STL files so perhaps try generating the STL files and convert to Gerber.
4. Lastly , export your design as a 2D PDF (or Postscript). Yes, ACE can convert any PDF file to Gerber and many universities/companies prefer this approach because of the simplicity. Here's our guide for converting PDF files to Gerber, https://www.numericalinnovations.com/pages/postscript-and-pdf-conversions-101
Thanks again, and I look forward to hearing from you. Always feel free to submit a support ticket and include your sample output from COMSOL - we'll be happy to create a custom tutorial movie showing exactly how to convert your files, https://support.numericalinnovations.com/support/tickets/new