Hello,
Yes, the variable in your region mask file should be in real format. You may straightforward use ncflint to convert them from integer to float or refer to Cristian’s suggestion, and see if your CMAQ/ISAM works.
Try to use m3fake instead of t3mask in t3tool, please refer to
https://forum.cmascenter.org/t/error-creating-gridmask
BTW, I created my mask files using ArcGIS and ncgen.
Thanks.