Given an RNA sequence having metastable secondary structures A,B, the program FFTbor2D computes the ensemble free energy E(x,y)=-RT log Z(x,y), taken over all secondary structures having base pair distance x from A,and base pair distance y from B. While the Vienna RNA Package program RNA2Dfold computes the ensemble free energy in time O(n7) and space O(n4), by employing the Fast Fourier Transform (FFT),FFTbor2D computes the same value in time O(n5) and space O(n3).