The five-time champion went into the quarter-final as the clear favourite, but suffered a 7-6 6-4 3-6 6-3 defeat.
"I've got to go back to the drawing board right now and see what is the priority [for the rest of the year]," ESPN quotes Federer as saying.
"I've said it 100 times; it's been amazing - I'm back to number one, I won Wimbledon, but we don't need to talk too much about that right now. I lost the match. A very disappointing match for me."
Federer went on to say that his automatic qualification in round four due to Mardy Fish's withdrawal may have had a negative impact.
"I should come in here with tons of energy, ready to go, but who knows? If you get that day in, that match with Fish, [it's] maybe more confidence, who knows?
"Maybe that was something that the first two matches didn't give me enough. I don't know."
Berdych will take on Great Britain's Andy Murray in the semi-final following his victory over Federer.