If it is a local notification then to remove badge icon you have to do it like this
UILocalNotification *localNotification = [[UILocalNotification alloc] init];
localNotification.applicationIconBadgeNumber = 1;
If it is push notification the you can do it by code written below
[UIApplication sharedApplication].applicationIconBadgeNumber=0;
You may call these methods anywhere you want. For example if you want to clear notification at the moment when the app is launched then write it in
- (BOOL)application:(UIApplication *)application didFinishLaunchingWithOptions:(NSDictionary *)launchOptions
if your app doesn't use the badge number you have to first set, then reset it to remove it from notification centre.
[[UIApplication sharedApplication] setApplicationIconBadgeNumber:1];
[[UIApplication sharedApplication] setApplicationIconBadgeNumber:0];