Thank you Aleksejs for those useful quick links.
I plan to use Omnikey 3021 card reader that runs in a web browser.
And this system will interact with the website when there is a need.
I think the best idea will be to implement java-applets that can read the data in smart cards using the Omnikey Hardware. And, it will send the authentication or other information to the website.
The problem is that the system should be a web-based application; and not a desktop application. But still, it should be able to read out the card in the customer's web browser and send information to the server.
The below links would help you understand what I need:
http://www.ugosweb.com/scemu.aspx (an example of java applet reading the card)
https://nihlogin.nih.gov/CertAuth/UsingSmartCardsWithNIHLogin.pdf (manaul to similar operation)
I am searching for some coding examples, API/DLLs or technical/programming articles to make this possible.