If your lease was properly drafted you can credit the rent payment first to the late fee and then to the actual rent. If the rent is not paid in full you would then be within your rights to serve a 3-day notice to pay or quit. Explain in the notice what happened and why money is still owed.
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Late fees are generally not considered rent, so a 3 day notice to pay rent or quit is probably improper. But if the tenant fails to pay a lawful late fee that is required by the rental agreement, then the tenant is still violating the rental agreement. The law permits you to serve a 3 day notice to perform covenants or quit (this is different than a 3 day notice to pay rent or quit) when the tenant violates the rental agreement. You should probably consult with an attorney before serving any such notice.
Depending on the language in your rental agreement, you may also be able to deduct the late fee from the security deposit and request the tenant to replenish the security deposit.
You may also consider a small claims court action against the tenant.