To the best of my knowledge, doing about 30-45 of aerobic exercise (running, stairs, swimming) at a controlled pace to keep a heart rate that isn't too elevated is what I have heard recommended for burning fat. At 45+ minutes, the prolonged higher levels of cortisol in your blood will start to burn protein from breaking down muscle tissue along with the glucose from fat. The greater the proportion of muscle to fat you have, the more it will favor muscle tissue as an easy energy source. I have no idea how many weeks/months it would take for an exercise routine to remodel your muscles however.
Perhaps you might want to try training for a marathon or triathlon, focusing on 3 days of long distance(MWF), and 2 days of High Intensity Interval Training (TuTh), and 2 day of rest per week(SaSu). Usually you'd do whatever anaerobic exercises you like on rest days or do yoga/Pilates after cardio workouts to keep from getting cramps. But because the goal is to lose muscle you might do one more HIIT session on one of the rest days. Supplementing the workout by performing multiple endurance sports can keep it interesting, like switching between running (or elliptical), cycling and swimming long distances. People tend to ease into the 5-6 day exercise plan by starting at 3 days and adding another the following week as long as it doesn't encroach on your daily energy.
Personally, I haven't worked out at this level since I was playing high school soccer, and this routine is incredibly demanding and time-consuming. I'm thinking of investing in a camelBak and getting back into an endurance routine myself, since I hate carrying my water in a messenger-bag.