There is no single answer for this. If you didn't buy a boot from a pro, expect to pay $50 to $125 for evaluation and consultation. That fee is normally credited if you bought the boots from the fitter and usually includes minor punches, grinds and pads. Additional work is sold based on complexity and time. Larger grinds, punches pads to accommodate anatomical anomalies might cost $20 - $50 per adjustment. Boot planing, shimming and alignment work may be $100. Foot-beds are dependent on type and complexity.
Consider these very rough guidelines. Each shop has its own business to run and walks the line between making a decent living, and losing customers to perceived excessive cost. If you look at bootfitting as a time and materials business like consulting, you will probably be pretty close.