Jawaduddin,
I am guessing you are using the OptiFDTD product, you should post your questions there to ensure the right person finds it. Your reflectance is obtained by ensuring that your observation line is in the correct place and by using the “Power Spectrum” in the Analyzer, this can be found under the “Tools” menu option.
If you were to provide your design file (fdt) I would be able to give you a better idea. Also please let me know what version of the product you are using.
Scott