Some tools only accept GTF. Some also accept GFF3 and those will have options on the tool forms where you can change the attributes to use when counting up reads versus features in the annotation.
Featurecounts happens to accept GFF3. So you need to do some adjustments.
Converting to GTF is also an option. See Working with GFF GFT GTF2 GFF3 reference annotation
This forum also has a LOT of troubleshooting about reference annotation. Search with tool names or datatypes. I also added some tags.
For the reference genome, see Reference genomes