Well, i am not so sure: according to the MSI website the Maximum CPU Cooler Length is 16 cm for the case and the cooler is 16.5 cm. I have a much bigger case with max 18.5 cm space, so it's not a problem. Maybe you can try the Noctua NH-U12A. It is lower, but similar performance. It all depends on your system. Or you need a bigger case. Before I bought all the components I checked it with the Noctua support, which one they recommend. Good luck! :-)

In first time should be work because all the mesurements are standard in all PC semi-tower / tower. Aside depends third party issues like if you use a liquid cooling for the graphic card (the tubes could be make interference in the air flow or installation).

My recommendation it's install the Noctua before install the mainboard to the chasis in the following order:

1. Install the power supply in the case and throw the cables backside of the case.
2. Install the processor, RAM and cooler in the mainboard.
3. Present the keyboard in the chasis in a possition hight where you can connect the electricity cables (the cooler dimensions will make you hard connect them).
4. With all connected put the MB with all in the case and install the screws

And have a long screwdriver with magnetic point (the top-right screw of the mainboard it's the most difficult one because the space of movement it's very limited).

Regards.