You'll have great big cylindrical modulators on either side of the bike, just above the footrests with the word "ABS" emblazoned on them.
Removing the rear fender will not affect the rear
brake in any way.
If you have normal brakes (non-ABS), then it's probably you have air in the system. Any small amount trapped somewhere in the system will exhibit the symptoms you see. The rear
brake needs to be bled to expel the air trapped in the lines. There are many threads on the subject of how to do such a
brake bleed if you search the forum.
Examine under the right footpeg plate to see whether there are obvious signs of fluid leakage from the master cylinder or the line that connects it to the rear caliper. These clues will point you to the problem. There aren't too many parts in the non-ABS back
brake system -- reservoir, master cylinder,
brake line, and caliper. Any leak in the reservoir will not contribute to a soft
brake pedal. Leakage from the front of the MC, from the straight connector at the rear of the MC, at the joint where the flex line meets the rigid line or at the caliper are the points where air can enter the system and cause a problem. If you have the original rubber
brake line, it's possible that it has reached EOL and needs to be replaced.