As Jefferson was the third President and the Federal Court system was designed to have life-time appointments, many of the original holders of Federal judicial posts were held by Federalist appointees who had not yet died in office or resigned.
So, Jefferson found himself waiting for turnover on the bench without much success.
Answer: The President in the executive branch can veto a law, but the legislative branch can override that veto with enough votes. The legislative branch has the power to approve Presidential nominations, control the budget, and can impeach the President and remove him or her from office.
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