When your payroll check is done, are the taxes calculated on total earnings – even with pre-tax deductions?

I have pre-tax medical and retirement taken out but when I calculate out how much of my total gross I take home, the percentages indicate the taxes are being calculated on total earnings, not the total after pre-tax deductions. I thought that was the benefit of pre-tax deductions – you didn’t get taxed on it. If anyone knows of the legal writings for payroll practices, I would like to know, thanks.