Slightly reformatted and ellipsized for easier (YMMV) comprehension, thinkdifferent wrote:

...I can run via command prompt by typing the following command:
rnafold <inputfile> outputfile.
now i want to run the program using perl.... i tried the following command...
#!C:/perl/bin/RNAfold qx/rnafold <inputfile> outputfile/;

You say "command" in both examples, but while the former apppears to be a valid, windows command line input, the latter looks like a borked fragment of a script. If you really mean you tried to type
#!C:/perl/bin/RNAfold qx/rnafold <inputfile> outputfile/; at a W32 command line to run a Windows "executable", the shebang isn't going to magically invoke Perl (in fact, IIRC, it should cause your system to spit an error to the general effect of "'#!C:/' is not a valid program"). What's more, even if that worked, the balance of the line isn't going to utilize qx/.../ without invoking perl.

So, please clarify: is the second example meant to be the code in some script you've created? ...Or is a case of making stuff up and hoping the computer will understand?