Students who have completed most, but not all of the prerequisite courses are encouraged to apply as long as they have a plan in place to complete the courses prior to the start of the MFE program to which they are applying. In fact, there is a question in the application that asks which courses the applicant plans to take prior to the MFE; this would be an appropriate place to list the plan of study.
The admissions committee will take your preparation plan into consideration when reviewing your file and if you are admitted, will track your progress through your preparation plan.