Just scuff the pad faces lightly with some 90 grit or so sandpaper, don't need to get to wild with the sanding. Install your pads and new rotors and do a few easy stops on a empty road from about 35mph or so and space stops out a minute or so apart to let the pads bed into the rotors, don't let them get too hot. Avoid hard stops if you can for awhile as the pads could glaze over and all should work out fine.
1966 Coupe w/ 351w
1969 Mach 1 S code (390 w shaker)
1984 SSP Ex Oregon State Police
1985 SSP Ex Oregon State Police
2012 Kona GT prem.