I created a script that monitors a Cisco Router interface.
./check_cisco Router1 Serial0/0/0
Interface Serial0/0/0 is up for Router1
I would like to stop all other notifications if a critical or warning alert is trigged for this alert. Not really sure how to do this.
You will have to look into the dependencies system of nagios.
See http://nagios.sourceforge.net/docs/3_0/dependencies.html
If you want to avoid warnings for hosts behind the router interface when it is down, you could simply use the "parents" option on the hosts behind it. This tells nagios that whenever the router is unavailable there is no use in checking the stuff behind it.
Adding "parents" to all your hosts has the added benefit that the status map becomes much more useful.