| but since my RNA has strong secondary structure, the reverse transcriptase cannot get through it |
That is a big assumption, and the least likely cause. The secondary structure can be there but really never seen it stop an RT-PCR.
reducing amount of RNA (likely cause of background)
Make sure RNA is best quality you can get (RNAse free, desalted, fresh)
1 primer only for transcription (low concentration so it gets used up)
reduce primer-dimer problem in PCR (reduce concentration of both primers, optimize #cycles, PCR-annealing temp, extension time etc).
After doing some or all of the above and if still in need of optimization:
you can pre-melt RNA (melting the 2nd structure really 95C for 30-50seconds) with primer (mixed/vortexed in RT rxn buffer only); very quick chill on ice, followed by adding rest of RT rxn mix and then beginning your RT rxn.
--A specific primer annealing should be facilitated and should improve your final results.