To prevent creating backup files, use generateBackupPoms
instead:
mvn versions:set -DgenerateBackupPoms=false -DnewVersion=3.9.0-SNAPSHOT
I also saw that you can set up generateBackupPoms in the plugin section of a pom.xml if you want to do it that way.
Note if you are using eclipse, you can run the command using a run configuration like this:
See also: http://www.mojohaus.org/versions-maven-plugin/set-mojo.html