As Hunter suggested, I do the same for the few pedals I have with rubber bases. Not wanting to mutilate the pedals by ripping off the rubber bases (I like keeping my gear as new as possible), I cut enough of the velcro to reach the top edges on both sides, that will hold them in place with plenty of strength.
There is a guitar parts website that offers replacement plain metal base plates for Boss and if memory serves correct, one or two other brands of pedals, so you can apply velcro.
Also, as someone earlier has mentioned, I have used blue painters tape on a Boss pedal and then applied the velcro on top of that which has held up to at home use. Not sure how it would hold up for traveling pedalboard. Cheapest method to try, though, without ripping off the rubber pad.