RNA secondary structure has become the most exploitable feature for ab initio detection of non-coding RNA (ncRNA) genes from genome sequences. Previous work has used Minimum Free Energy (MFE) based methods developed to identify ncRNAs by measuring sequence fold stability and certainty. However, these methods yielded variable performances across different ncRNA species. Designing novel reliable structural measures will help to develop effective ncRNA gene finding tools. This paper introduces a new RNA structural measure based on a novel RNA secondary structure ensemble constrained by characteristics of native RNA tertiary structures. The new method makes it possible to achieve a performance leap from the previous structure-based methods. Test results on standard ncRNA datasets (benchmarks) demonstrate that this method can effectively separate most ncRNAs families from genome backgrounds.