If you mean "running under" that you have subapplications (they show with a colored icon) that run under the site then you can stop the app pool it runs under. You can quickly figure this out by right clicking the "app" in IIS Manager and seeing if it says "Convert to Application". If it has that option then it isn't an app.
If the app is running under a shared app pool then you have to stop all apps running under that app pool. That is why it is generally recommended that you don't use subapps and that, if you do, then you run them in separate app pools.
If the "app" is a virtual folder (not an application) then you cannot stop it because it is simply a folder under the main site. You would have to stop the whole site to make it inaccessible.For ASP.NET apps you can also take the app offline by dropping an App Offline file into the root directory. This doesn't stop the app but prevents people from accessing it.