Stronghold is not just a prison for super-powered criminals; it is a maximum-security prison for supervillains; not all villains will be placed here just because they have powers. Still, with at least a half-dozen villain books, not to mention the scores I've made myself, there are three Strongholds in the Megacity campaign (none of which are actually in Megacity) - the original one in the Arizona Desert, one on the moon called Lunarhold (derogatorily referred to as the Lunatarium), and another in the middle of the Atlantic Ocean, officially termed Stronghold Atlantis (derogatorily called Neo-Alcatraz). Some of these stats are useful for all of them, where others are specific to the hold.
When deciding which Stronghold is appropriate for the villain, consider his abilities and choose the one which will impede him most. For example, if his abilities include anything to do with water, the desert is most apropos; those with space-travelling powers will likely not be held in Lunarhold; and so on.
All of the strongholds are multilevel, as the GM decrees, with the Basement or uppermost Level housing the control center and the Subbasement (or Basement) Level being a wide-open storage facility and hangar. In all cases, Room 1 (note Stronghold layout sheet) is a temporary holding room where prisoners are processed, for both entry and release. This is where prisoners are held while Power Suppression Units are adjusted for them. As noted on the Stronghold layout sheet (included in the Champions/HERO System Rulesbook), there is a small control center in the very middle of the complex, as well. All the levels extend to the center of the stronghold and stop short, leaving an open shaft from roof to floor (excluding Basement area[s]). Technically, this area contains the gears and mechanics needed to control each floor; the actual, computerized controls (the software of the system, if you like) are accessible only through the main control room and can be overridden only from there (Security Systems Check at -7). Characters may be able to "throw a wrench" into the mechanics (the hardware) by affecting the controls located at the center of each stronghold. This will only affect one or two operations (such as the gates or cell doors) on one floor or the like and should be determined by the GM as appropriate for the game.
Of course, this shaft is off-limits to prisoners and most personnel. Access is via man-sized doors, controlled by electronic lock from the control center. The walls have the same stats as the outer stronghold walls (q.v.).