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my 3 year old red eared slider constantly rubs the top of his shell on the heater, he does it sometimes for 5 minutes straight.

is this bad? why is he doing it?

Sometimes turtles will rub their shells against objects when the scutes are getting ready to shed (it helps them to come off). Do any of your turtle's scutes look like they're getting loose (whitish color, air bubbles under the top scute, water seeping out of the sides when you gently press on them, etc.)?

Yes that sounds about rite, i thought it could of been worse, like a Very irritating internal itch, but last night i took him out and softly massaged his shell, after that he didnt rub it anymore

Many turtles like to get back scratches from their owners when they're getting ready to shed. ^_^

Mine does sometimes, but it's hard for me to do it softly because he's so small.