Your description of what is happening is very confusing.
A furnace that has a dirty air filter or other obstructions in the return or supply ducts will shut the burners off on "high-limit". It will then re-fire again after a short time (maybe 1-2 minutes) and then shut down again on hi-limit. The fan usually will continue to operate when this hi-limit burner shut down occurs.
Is this what is happening?
Post back with some definite detail and we will try and give some help.