private void button1_Click(object sender, System.EventArgs e)
{
      TopologyManager myTopologyManager = new TopologyManager();
      PortalSite myPortalSite = myTopologyManager.PortalSites[new Uri(textBox1.Text)];
      try
      {
            //You can also specify a bool of true here if you wish to remove the databases
            myTopologyManager.PortalSites.Delete(myPortalSite); 
      }
      catch (Exception ex)
      {
            listBox2.Items.Add(ex.Message);
      }
}

Here is some alerts based code just to get you in the right direction.  If you knew a specific alert ID you could operate against it--or you could enumerate all, look for something specific and then act accordingly.  Here is an example on doing a mass removal.  I have never had to use this... I doubt I would want to because I would want to enumerate and have some more control.

      //using Microsoft.SharePoint.Portal.Alerts
      Administration myAlertsAdministration = new Administration();
      myAlertsAdministration.DeleteAllSubscriptions();

Here is a quick sample on enumerating alerts within Portal and doing a variety of non-specific tasks (which of course you wouldn't do all at once).  Here I get to show one of the many entrypoints that utilizes PortalContext.

      //using Microsoft.SharePoint.Portal.UserProfiles
      UserProfileManager myUserProfileManager = new UserProfileManager(myPortalContext);
      UserProfile tempUserProfile = myUserProfileManager.GetUserProfile(textBox1.Text);
      foreach (UserProfile myUserProfile in myUserProfileManager)
      {
            myUserProfile.Alerts.ActivateAll();
            myUserProfile.Alerts.DeactivateAll();
            myUserProfile.Alerts.DeleteAllResults();
            myUserProfile.Alerts.DeleteAll();
      }

As you can imagine, there are a number of possibilities here in what and how you can accomplish your specific task.  You could even add alerts programatically with a little finesse.