Jeremie,
Military Training can be broken down into two major components. Running/Endurance and Calisthenics. But since you want to focus on muscle building I would focus on more of the calisthenics if you want to stick to a "military" style.
I would still do some sort of cardio on days you don't do a calisthenic routine, like interval runs, or sprints, or a fast 3 mile run, but thats up to you.
For a routine I would do a 3 day full body split with pushups, pullups, squats, lunges, ab work and variations of those. If your gym has a TRX system, I highly recomend using that. To give you a little idea of what it could be google MARSOC Short Card. You could create your own plan using tabata, circuits, or typical sets and reps. Its up to you and your training preferences.
One workout my platoon likes to do is a half mile-mile fast run (6min/mile pace) followed by 15 pull-ups 10 diamond pushups and a core exersise, and we would usually do that 4-5 times. We also do something we call "Club Muscle." It's basically a set amount of pullups, 10 dips, 10 pushups, 10 squats, and core exersise. sometimes we do 3 sets of 12 pullups, drop to 3 of 8 and then 3 of 6. Other times we do 6 sets of 10 pullups or pyramid sets of pullups, but always followed by the same amount of dips, pushups, and squats. The core exersise varies on what it is wether its flutter kicks (usually 25-50 4 count) or planks (90sec front, 45sec side) or Chinese situps (15 1 count).
It all just really depends on you and what you want to do.
I hope this helps you out.
-Jacob