Can you tell us more about the 36V motor?
Without any information, I would suggest that the 36V motor would run directly from 48V with no problems.
That still leaves the 9V.
But 33% over voltage on a motor might be a bit much.
If the battery is based on separate accessible cells then tapping the individual cells could be an option but leaves some of the cells unused, unless you can live with a positive and negative power supply. Otherwise it would require to separate the batteries, but that might cause problems with the battery management system in case of lithium ion cells.
The easiest option would be to use two buck converters. One to make the 36V and another one to make the 9V. It does depend on current draw which buck converter suits the bill. A motor can draw quite a bit of current certainly at startup and the converter needs to be able to handle this without dying.
So to make better suggestions more information about both parts of the system are needed. (So info about the motor and the microcontroller system that is)
Edit: Forgot to mention to also include more information about the battery.