Results: In this paper we present the inverse folding algorithm {\tt inv} as well as two applications. We give a detailed analysis of {\tt inv}, including pseudocodes. The algorithm is freely available at \url{http://www.combinatorics.cn/cbpc/inv.html}. We show, using 3-noncrossing nonplanar RNA pseudoknot structures as an example, that {\tt inv} allows to design specific 3-noncrossing RNA structures. Furthermore we use {\tt inv} for estimating the distance of the neutral networks. Conclusions: The algorithm {\tt inv} extends inverse folding capabilities to RNA pseudoknot structures. In comparison with {\tt RNAinverse} it uses new ideas, for instance by taking sets of competing structures into consideration. As a result, {\tt inv} is able to find novel sequences even for RNA secondary structures.