Apple TV, like many other set top boxes and home theater components, comes with its own separate remote. This aluminum remote is much smaller than most other remotes, making it easier to lose. But there are other ways to control the Apple TV, including an option to use one of your existing remotes.
iOS Remote App
Apple has a free remote app for both iPhone and iPad that you can pair with Apple TV. This does everything the regular remote does, and more. Not only can you easily navigate through Apple TV's menus, but it will utilize the on-screen keyboard for typing in passwords and search queries. The remote app is free in the App Store.
Program Your Existing Remote
Go into Settings > General > Remotes. This shows you all of the remotes, including iOS devices, paired to the Apple TV. Scroll down to "Learn Remote", hit enter, and then select "Start" to begin the process.
Next, press and hold the button on your remote that corresponds with the action being shown on screen. You'll see a progress bar as the Apple TV learns each button. After you set up the basic buttons, you'll have an option to continue and setup the "Playback Buttons." If your remote has Play, Pause, Rewind and Fast Forward buttons, you can set those up to work with Apple TV.
Once it's complete, you'll be able to name the remote, and it will show up in the list of paired remotes on the Apple TV. If you'd like to edit or unpair the buttons on the remote, scroll down to it in the list of paired remotes and hit enter. You'll be able to re-configure it or delete it there.
If possible, it's best to choose buttons that you wouldn't be using with anything else on your TV. Otherwise, you could end up sending signals to the the Apple TV while controlling your TV or a different component in your home theater system.