How to keep away trojan codes?

i manage a site, coded in asp.net. Days ago when I click to the pages, there are pop-ups and reported by nod 32 as a virus page.  Later i find some alien codes in the template for the home page and categories, they are coded in <em>. as these strange codes are cleared, web pages are normal again.
I'm worried that the codes may come back. What could I do to protect my site ? Many thanks.

Avoid saving your FTP connections on your computer but rather change them in your hosting panel at least once a week and alter some of the attributes on the files found which are existing in your server.

agree with your answer, todays i am working on molware viruse in trojan, it will complete in next week

Keep away from economy your FTP relations on your computer but quite change them in your hosting board at smallest amount once a week and alter some of the attribute on the files found which are obtainable in your wine waiter.

agree with your answer, todays i am working on molware viruse in trojan, it will complete in next week

you never remember password in any file protocol software
such very difficult to determine solution for anyone because everybody have own mind and works for our benefits therefore everything is infected.

Make sure you use hosting that protects you from such attacks like SolidShellSecurity.com and keep your site script updated and passwords safe.