You will probably have to discuss this with your IT department as there are several security aspects involved and the specifics will depend on your infrastructure.

One solution could be to install one of your FME Server instances in the DMZ, I would also strongly recommend activating SSL. Using a reverse proxy could also be something to consider.

Thanks, we want to access data upload and download folder web accessible. I configured the config.txt where i have changed the upload/download directory to a web server but this is not working.

As David has mentioned, your best bet is to involve someone in your IT department to be involved as they will have a good understanding of what can and can't be done in your environment (which could be different then the next company). The reverse proxy is often helpful in achieving this.

If you want to show the FME Server web interface, solution proposed by @david_r is the way to go. Otherwise, if you already have a web server visible to the outside, you can add a web page who will benefit of the already defined IT security and let back end code interact with FME Server and serve the results without having to move your FME Server in the DMZ.