Timber above waterline may provide aesthetic value depending on your personal perspective, but also serves as perches for cormorants, pelicans, ospreys, eagles, etc. I understand both sides of the issue - and your desire to cut them at the waterline is what Mike Otto recommends to his customers.

If you choose to cut them, I second Flame's suggestion using a stable platform - a floating dock moved with trolling motor sounds like a good approach.

Many men go fishing all of their lives without knowing that it is not fish they are after. ~ Henry David Thoreau

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