The only true way to get all of the old fluid out of the hydraulic/hydrostatic system is to remove all of the hoses, cycle and clean all of the cylinders, pumps and motors. Don't forget to clean out the fluid tank. Metal will settle at the bottom When the machine sits idle.
You can try to clean most of it out by removing all of the fluid from the tank and cylinders. The cylinders hold a lot of fluid and you can remove the hoses from them and one pin so that you can cycle them to get all of the fluid out. Also remove all of the hoses from the drive motors so that the fluid can drain out of the motors and hoses. Remove the quick couplers and hoses from the auxiliaries and let them drain also. And clean out the tank. After all of that is complete, put in all new filters and refill and cycle everything till the system is full. Then do a regular maintenance fluid change and change all of the filters again.
These machines were never designed to be completely drained. If the machine is old enough you may just want to go ahead and change out all of the hoses to new since you will need to disconnect most of them anyway.