The plugin uses signs to show the lint errors. If you never want to see them
let g:pymode_lint_signs = 0
disables them.
If you want to clear them, AFAICT there's no interface in the plugin for just that. (You could file an enhancement request.) But what should work is clearing all signs of the current buffer:
:sign unplace * buffer=<C-r>=bufnr('')<CR>
or
:execute 'sign unplace * buffer=' . bufnr('')