I had this problem when I was applying for US citizenship. I was on the crew team in college, which means I had callouses all the time on my fingers, and thus blank fingerpads.

I applied for citizenship 3 times over a period of 3 years, and each time got rejected due to poor quality of fingerprints.

Finally I stopped rowing and then got my citizenship. I'm sure there's some way around it, but it was kind of amusing and frustrating at the time.