Baylor University has recently digitized the maps in the book titled 1895 War of the Rebellion Atlas. The collection contain 175 plates with verbal descriptions of the contents of each place. The collection is searchable.
The URL mentioned below will take you to a page where you can browse the collection by state, city, or body of water. You can also do a search using the box that appears in the upper right of the page. Once you find a map you are interested in, click on the small image of it. That will take you to a description of the map contents and other information. To get to the large image of the map, click on the "Access this item" hot link that is at the top center of the page.
This is a great resource if you are doing research on battles your Civil War ancestors participated in. Check it out at http://goo.gl/k1zRH