I lost my generation three Apple TV remote can I use an app without a TV remote

If you have a 4th Generation Apple TV, you can setup the Remote App without the physical remote.

with earlier Apple Tvs, unless you had set the App up previously when you still had the remote, you cannot.

You need the physical remote to navigate to the setup screen on the 2nd and 3rd generation Apple TVs

Instructions here:

Set up the Apple TV Remote app - Apple Support

Welcome to the Apple Community.

My best advice, in my opinion, is to recommend you purchase a replacement remote, however, if you are averse to this suggestion there are some workarounds which may apply in some situations.

Depending on which Apple TV you have you may be able to set up the Apple TV from your mobile device. You will need a 3rd generation Apple TV for later running software version 6.0 or later and an iOS device running iOS 9.1 or later.

Restore your Apple TV. When the Apple TV setup screen appears, unlock your iOS device and make sure Bluetooth and Wi-Fi are turned on. Touch your iOS device to Apple TV and follow the onscreen instructions on your iOS device and Apple TV.

Automatic setup doesn’t transfer account information for third-party apps such as Netflix or Hulu and doesn’t turn on iTunes Match or Home Sharing.

If this doesn't work, you don't have an iOS mobile device or your equipment doesn't meet the minimum requirements, you may wish to look at ciderTV for Mac OSX, once you have installed the app on your Mac...

1. Check that Bluetooth is On & Discoverable;
2. Keep Bluetooth preferences window open during pairing;
3. Connect Apple TV to your Mac via USB cable and reset it in iTunes app;
4. Turn Apple TV on and wait until it finds your Mac. A pop-up window will appear that says “Pairing Request from Apple TV”;
5. Tap "Pair";
6. You will see CiderTV control interface with buttons.