You have to get the HM Cut from the Captain of the ship in Vermillion City.
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bidoof and bibarel can cut trees
get cut from the cut master in the city w/ the first gym and Devon inc
You have to get the hm, then, you have to beat bugsy, the Azalea town gym leader. After that, teach it to one of your Pokemon so you can cut down trees.
You get HM01 Cut from Ilex Forest. Use that to cut down trees.
Teach HM Cut to a Pokemon and use it on the tree.