The FRACTAL R3 case has space for front intake fans, rear exhaust and roof exhaust.
Heat shouldn't be any issue at all. The only thing that might make a small difference was if the case has a side fan to blow cold air directly onto your GPU.
Either way MSI cards have their own great cooling fans and heat should never be an issue even when pushing the card to its limits. http://www.bit-tech.net/hardware/cases/2010/10/29/fractal-design-define-r3-review/2