Depends on how you have implemented the withdrawal. I can see two options: through a smart contract or your backend issuing a transaction to send Ether from a wallet.
1) Through a smart contract
If the user initializes the withdrawal, they have to pay the transaction fee and it doesn't make sense to reduce the amount of Ether they get. If you initialize the withdrawal, you have to analyze how much gas the transaction requires and you can reduce the sent Ether based on that.
2) Backend issuing a transaction
In this case there is no smart contract involved and your backend system (not inside the blockchain) sends a transaction to tranfer the Ether to the user's wallet. You can use http://ethgasstation.info/ to estimate how much the transfer costs.