MODULE 2: Epilepsy Medication Therapy 12 Possible Medication Challenges Your doctors consider several things when choosing medications to treat your epilepsy. You may face some challenges as you and your healthcare team work together to find the right medications and dosage schedule for you.2 AEDs work best if they are taken regularly as prescribed by your doctor.7,13 It’s important for you to understand your own personal reasons for taking your AEDs regularly.