Per hour, per man. Or per hour, per machine. This is an unusual scenario, though. It seems no one around here trusts a tree company to work hard on an hourly basis.
All this kind of work that I have done (except for big contracts) is by the job. I then walk through the entire project and divide the job up into as many details as I can. Usually I count all the trees and divide into 3 sizes. After I have looked at everything, then I assign a price for each size of tree removal based on the difficulties on site. Multiply tree value times your tree count.
Add roadtime to and fro, equipment mobilization, disposal charges if any. Add a "wasted time" factor to help cover the probable losses. Then add it all up.
That was method #1.
Method #2: break the job into acres/day or square feet per day, given the crew and equipment that you will likely use. This is very helpful if you have similar jobs to compare it with. Figure out how long you will be there, multiply by your rate per hour for your crew. Add in roadtime, disposal charges, and breakdown time.
Method #3: form a wild-ass guess as to how much you think it is worth, tempered your previous experience and by what the customer will probably be willing to pay. It helps to know what the competition is likely to bid.
Compare notes & prices on methods 1,2, and 3. Tweak numbers on all of them until you decide what to bid. By comparing different methods, you will likely reveal glaring faults in any one method. If the final bids are all wildly different, you haven't thought about it enough.