I have a Bryant gas furnace Model Plus 90i 355MAV. When it runs in high heat mode for several minutes it makes this thumping sound that seems to be coming from the blower area, after a couple of seconds the furnace shuts down. Any Help? Unit is about 6 years old

Well first of all I would check the blower for

Paper or other debris that might have got stuck in the cage fan area.
Check the cage fan for loosness
Check the motor mounts/bolts and where the motor band is bolted
Check the motor shaft for end play
Check that the housing is still bolted securly to the units slide bracket ETC

TURN OFF POWER before service!! OR you will get your fingers cut off by the spinning wheel also watch for sharp edges on the metal.

Post back with results.

The thumping sound is coming from the blower motor. Unit makes sound even in fan mode. When running in hi speed motor starts to vibrate then the unit tries to shut down. I have been searching online for new motors and have discovered that my motor has a built in speed controller, will I need to replace both the motor and the speed controller or just the motor?

Usually just the motor. BUT

If there is a good motor shop locally you might have them look at it. The reason is those motors are very expensive and they might be able to just replace the bearings.

Make sure the motor mount system is good. This can also cause motor vibration.

A overall inspection of the motor needs to be done also the spinning cage that is attached to the motor can also go out of balance causing a bad vibration.

All of these items can be very expensive as you will find out that is why I recommend someone with experience in these motors actually look at what you have to be sure everything that needs to be replaced is taken care of so the problem does not come back to soon. These variable speed motors promise energy savings but the parts for replacement cost more than the energy saved. Around here most of those motor systems are scrapped and a regular 3 or 4 speed motor is installed since it is so much cheaper. But that entails a conversion and that takes hands on knowledge as to how do to do it on site. Good luck with your project.