If I convert the same file to UTF-8 in windows , FTP to the UNIX and use the file command it shows as 'UTF-8 Unicode text'. But why its not happening when I use the iconv command ?
Could try a unix "diff" on the unix version against the Windows version and see if there are any significant differences.
If the file is something like XML format, the unix command "iconv" is not suitable.
It's hard to be specific without knowing what Operating System and version you have and something about your data and your Windows process.