Build and Runes
Miss Fortune is very vulnerable when she is channeling her ultimate. Either focus her or disable (stun/silence/knock-up/displacement) her.
Avoid trading with Miss Fortune for an extended amount of time, as she will do more damage with her Impure Shots with every auto attack.
Try to keep her passive down by doing short frequent pokes and harassments.
Miss Fortune’s Impure Shots active makes her auto-attacks apply Grievous Wounds to the targets she hits. Do not rely on out-sustaining her in the form of healing, health regeneration or life-steal.