How does one physically prepare for an extended hike? Most people, if they are heavy, will attempt to drop weight and work out. Many in decent shape will do more running, or jump on a treadmill. All of this is good, but there is something else you need to do.
Take a look at the pictures. In the one with the blaze on the tree, that is the actual trail to the left of the blaze. This is a particularly rocky section of the AT in Pennsylvania. No matter how many times you jog around the high school track, your legs and feet are not prepared for this. Nor roots. Roots are everywhere and anywhere–even on rocks like shown above. Tip: Start backpacking in fields, forests, and parklands near you, and build up to shakedown hikes over diverse terrain.
This way your legs and body adapt to field conditions. Although I haven’t done it, I think climbing up and down stairs in a stadium, with your backpack, will help you if you live in the city. Best of all, build yourself up to a full backpack with all attachments (tent, sleeping pad, etc.) and get outside and go. Don’t do too much, too soon, too fast; build yourself up.