seam filler question

the section of the car covered by the rear of the front fender where it meets the door had filler around the seams. I could see rust so I pulled this stuff up and yep, rust. got it. The right side has filler but with paint on it. Should I pull that up too for a look see? Also, on the right side, from the top hood hinge post down, looks like Chrsyler dumped a combo of oatmeal and pancake batter down the side of the car. It comes up, is yellowish brown, and seems to have fibers in it.What a job. Do I need to replace this fille once I dig it out and primer and paint those sections? thanks eveyrone