Affectionate physical contact with the opposite sex is prohibited. For reasons of health care, there is room to permit professional physical contact. There is also room for leniency when such contact is part of training for a health care profession. During training, one should try as much as possible to partner with another female. These are general guidelines. Each specific situation should be discussed with a rabbi.
I suggest that you discuss in detail with each school what its requirements and policies are. We have heard of PT schools that insist that their students work with other students of the opposite sex, even for therapy maneuvers that involve being scantily clad or touching more intimate areas of the body. Other schools are more accommodating to students who request to work with a partner of the same gender.
While you will want to choose a school that is sensitive to your religious concerns, you should be aware that many of the patients you will care for professionally will be male (unless you will work with pediatrics or in an all-female practice). Therefore, it is important to do some work with male students during training, since you need to practice on someone before trying a technique on a live patient. You should also realize that uncomfortable situations do arise, both in training and in professional practice. Particularly in hospital and nursing home settings, therapists may be dealing with adult diapers, catheters, or even patients who exhibit inappropriate behavior due to cognitive issues.
You may find it helpful to speak with a religious female therapist in your area, and possibly try to spend some time volunteering with her to see how to deal with these issues on a practical level.