Heat pipes

[Ahhlong]

I recently bought a MSI GTX 760 and i realise that the heat pipes  are smooth but that this one part that the heat pipe is kinda  rough. will if affect performance?

 

[SMURG]

As long as the rough part is not in contact with the heating/cooling surface, no. As the name implies, a heat pipe is just a pipe for a liquid coolant inside. The coolant isn't pumped anywhere, it just takes heat from the solid encasing substance and transfers it somewhere else by convection and conduction. As the other end of the pipe is cooled, it draws heat from the area being heated, so as long as the rough part isn't in contact with either terminal (thereby having an impact on surface area) it really doesn't matter too much.