You will start by lying on your left side with your back toward the doctor. Most EUS examinations of the rectum generally take less than 45 minutes. You should know that if a needle biopsy of a lesion or drainage of a cyst is performed during the EUS, then the procedure will be longer and may take up to two hours.heck with your doctor about which medications you should take the morning of the EUS examination, and take only essential medications with a small sip of water. If you have an allergy to latex, you should inform your doctor prior to your test.