Mix a mild solution of bleach and water, dip a sponge into the solution and wipe out the inside of the trunk. Dry with paper towels or a rag. Alternatively, you substitute a half a cup of baking soda for the bleach. Keep the trunk open to dry out and air.
Place an open container of baking powder in the trunk and see if this helps get rid of the musty odor over time.
You can also try putting charcoal in a coffee can inside the truck also, you really need to find the cause of it, leave the truck open for a couple of days as often as possible. You can also spray the trunk with pure bleach and leave open to air out also.