To get rid of the old TIM, I just use Isopropanol spray or Surgical / White Spirit. Comes straight off.
I haven't used MX-3 but I do use MX-2 and I just spread it around with whatever is handy, even the edge of the tube if needs be. If going for the spread over surface of chip method, the anything flat will do.
Or you could go for the blob method and stick half to a whole pea size blob in the middle of the chip and the preasure of mounting it will spread the TIM for you.
CPU: Intel Core i5 2500K @ 4700mhz - 47 x 100MHz
Mobo: MSI P67A GD65
GPU: EVGA GTX 570
RAM: 2 x 4GB Mushkin LV 1.35v 1600MHz DDR3
HDD: 3 x 1TB Samsung Spinpoint F3's
Case: CoolerMaster ATCS 840 - Custom House of Kolor paint job.
PSU: Corsair HX750
Cooling: Custom WC - XSPC Delta V3, PA120.3, DDC Ultra with XSPC Res Top, 3/8" XSPC UV Green Tubing over 1/2" Barbs
OS: Windows 7 Enterprise Edition 64-Bit