We have several employees who are also patients. Is there any way that we can provide better confidentiality to our employees so that their medical histories are not viewed by other employees at transcription, check out, filing, and so on?

I actually don’t think you should change your work flow to accommodate employee-patients. I think you should stop seeing them. Their confidentiality is at greater risk than that of an average patient. They may want to withhold medical information you need because of their dual role, and it gets icky when you ask them to pay. I think you should refer these patients to physicians you trust. 

If you do keep them, the only way to protect them from the usual work flow is to handle all of the business-related issues yourself or to delegate them to your manager.