Gerbers are (usually) for graphical layers, such as copper, silkscreen, solder mask, etc. They're not usually used for drill holes, other than for a human-readable mark-up layer. Have a look into whether you can get Excellon drill files out of whatever your source is; FlatCAM will read those (though check Common Issues/etc about known scaling problems due to variable Excellon output depending on the sw in question).
Just to add a bit to XUHX's post ... 1. Excellon is BARELY a standard. It's rather like the pirate's code in those Johnny Depp movies .. more of a series of suggestions. FlatCAM wants TEXT format drill files, while EXCELLON is frequently output as a binary file. Ensure you have TEXT output. 2. FlatCAM wants a proper header for the drill file. My software output (for a PCB with two drills) looks like M48 T01F00S00 T02F00S00 which will not load into FlatCAM. I had to write a small program to tweak the output of my PCB program, such that the header now looks like M48 T01F00S00C.040 T02F00S00C.060 Basically, I needed to add the drill size to the definitions. 3. FlatCAM is picky about precision, that is, the number of digits used to describe a location. I think there is in the current version a way to configure this, but when I wrote the program above, I also added code to make FlatCAM happy. Stock from PCB program % T01 X00425Y0025 After my tweak % T01 X004250Y002500 Note the extra zero or zeroes. But it all works fine! I have purchased a number of "outliner" programs over the years and have now tossed them all. With one TINY exception, FlatCAM works perfectly for me.