I had the same situation about 20 years ago. The skid trails I inherited were really rough. Some still are. They are evolving into good tractor roads over time. I work on them slowly. First I made them into 4 wheeler roads so I could get around. I removed the downed logs and slash and cut the stumps as close to the ground as I could to do this. Just needed a chain saw. Once I could get the wheeler around I started mowing them with a trail mower to keep the berry bushes and stump sprouts under control. That thing can go a lot of places a tractor and bushhog can't.
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Then I just started using the roads with the tractor if I could. ( I had boulders, holes, skidder ruts, and steep side hill slopes to deal with also which stopped the tractor ). After a few years all those little stumps just sort of disappeared or got pulled up skidding logs over them with the tractor. I ended up with trails like this
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I finally bought a small dozer to fix the problems on the roads I couldn't get the tractor on. The rake makes the small stumps easy to deal with. If you really want to get your small stumps out rent or hire one of these.
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This is just what I did. Maybe you can get some ideas from it.
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