One of the saddest facts about the War Between the States is that technological warfare far outweighed medical advances. Many soldiers, after being shot by a minie ball, had to succumb to amputation or die from gangrene. There was no known remedy for infection at the time.
Some medical practices were downright barbaric, although bleeding had become obsolete by the mid 19th century. Leeches are used for this purpose now, interestingly. Halfway during the Civil War, it was discovered that maggots actually did good in that they devoured infected flesh, so they were intentionally placed on the soldiers for that reason.
Doctors considered infection a good sign, and referred to it as "laudible puss." They had no idea that viruses could be spread between people, or that insects carried diseases. People during the time thought that the air or the ground was contaminated, and that is how illnesses were spread. They were vaguely aware of germs and sanitation.
Many Civil War reenactments across the country are now including medical demonstrations, so that school groups and visitors can experience what a soldier's life was like, including the suffering they endured at the hands of physicians. I highly recommend that you attend one if you get the chance. Please check out www.reenactmenthq.com for a list of reenactments. You can also find an extensive list at www.civilwarcourier.com.