This is pretty simple, so basically when I'm trying to automatically chop trees alot of them have floating blocks that the bot does not get. Is there a way to get it to mine an entire tree? Thanks.

if you use the #mine command no baritone will go after the "cheapest" (easiest to reach) blocks that mach the parameter.
what you can do is to create a selection (#sel pos1 x y z and #sel pos2 x y z) and then use the #sel replace block1 block2 command to replace all instances of block1 with block2 example #sel replace oak_log air