We have two web applications of which one is configured with adfs and it is working fine but the problem is with sign out. When user clicks on sign out it is still staying in the site. Since we have configured adfs for two web apps i cannot modify the welcome .ascx in /_layouts . Is there a way I can make the users sign out from the site .
I'm not sure you can do that with SharePoint. You will have a "claim" from ADFS that will allow you to get into both your web applications. When you sign out of SharePoint, ADFS doesn't know that (unless you modify the sign out form to pass you over to ADFS sign out).
So when you access the web app again - you simply pass the token you already have.
You could potentially create a custom solution only for the web app in question which overrides the default signout behavior and redirects user to the ADFS logout page which will remove the cookies/tokens (thus granting you a true sing out).
Also keep in mind depending on how you have things configured with ADFS/SharePoint and the browsers - you may still experience something that looks like you never signed out, but in reality your browser is just resending the NTLM token to ADFS and logging you on automatically.