zero padding and window function of fft

i'm trying to do match filter with mkl. Zero padding and window function are two common tricks. I used to creating a new pointer and writing a loop to do the two process. But I find it very inefficient. The time of zeros padding and adding window function is three times as long as FFT (multiple kernel). So I want to know is there any efficient ways to do zero padding and adding window function?

Thank you!