"이 약은 하루에 세번 복용하세요."
Translation:Take this medicine three times a day.
It could be marked as a direct object. It isn't really necessary, because the verb means to take as in medicine.
The topic particle (은/는) does not mark the subject. It marks a topic, which can be a subject or a direct object or a location or a time. For declarative verbs (statements), the subject (if not stated) will often be assumed to be the topic unless the verb or something else about the sentence or context says otherwise. But for imperative verbs (commands), such as this one, the subject is always the person being commanded.
If I were a doctor telling a patient to take some kind of medicine, if that's it, I would probably use 약을 (or just 약). But if I'm giving instructions for multiple kinds of medications, I would certainly use 약은 because it would be necessary to explicitly separate the topic. "Take this medicine once a day with food. Take this medicine three times a day. Take this medicine two hours before you go to bed." I would use the topic marker every time.