MultiChain sets the transaction fee automatically based on the transaction size and the relevant blockchain parameters.
If you want to set the fee manually for a transaction, you can use the createrawtransaction API to explicitly state how much goes to the destination address, and the rest will automatically be considered as a fee.
To make life easier you might want to use preparelockunspent(from) first, to have the total amount you need ready in a single output for spending in createrawtransaction.