Refer to http://blogs.msdn.com/dwinter/archive/2005/02/15/373076.aspx for setup if you are not familiar with creating a SharePoint OM application.

This is a simple example of removal of all alerts registered in a site.  This can be handy for testing or mass cleanup. 

private void button1_Click(object sender, System.EventArgs e)
{
      //delete all alerts in entire site
      using(SPSite mysite = new SPSite(this.textBox1.Text))
      {
            foreach (SPWeb myWeb in mysite.AllWebs)
            {
                  foreach(SPAlert myAlert in myWeb.Alerts)
                  {
                        try
                        {
                              myWeb.Alerts.Delete(myAlert.ID);
                        }
                        catch (Exception ex)
                        {
                              this.textBox2.Text = ex.Message+"\nError deleting "+myAlert.User.LoginName+" Alert:" + myAlert.ListUrl;
                        }
                  }
            }
      }