How to write a CAML Query so that the result contains Column1 and Column2

Everyone is close, but not quite right.

using (SPSite site = new SPSite("http://server/site"))
{
  SPWeb web = site.RootWeb; // See disposal guidance http://blogs.msdn.com/b/rogerla/archive/2008/10/04/updated-spsite-rootweb-dispose-guidance.aspx

  SPQuery query = new SPQuery();
  query.Query = @"
          <Where>
            <BeginsWith>
              <FieldRef Name='ContentTypeId' />
              <Value Type='ContentTypeId'>0x0120</Value>
            </BeginsWith>
          </Where>";
  query.ViewAttributes = "Scope='RecursiveAll'";
  SPList list = web.Lists[listId];
  SPListItemCollection items = list.GetItems(query);
  // Do stuff with your folders
}

First of all, using this FieldRef is wrong:

<FieldRef Name='ContentType' /><Value Type='Text'>Folder</Value>

because the folder content type can be inherited. Therefore, you need to compare against the content type ID, like this:

<Where>
  <BeginsWith>
    <FieldRef Name='ContentTypeId' />
    <Value Type='ContentTypeId'>0x0120</Value>
  </BeginsWith>
</Where>

And then, set the view attribute Scope to RecursiveAll

<View Scope='RecursiveAll'>...</View>

That should return any item whose content type inherits from Folder (0x0120)

<Query>
  <Where>
    <IsNotNull>
       <FieldRef Name='Project'/>
    </IsNotNull>
  </Where>
</Query>

Is working for me.You should use U2U CAML Query Builder to build the Query by using the Designer.. It automatically generates the required CAML expression for you.

Can you provide more from your context. What are your settings on the SPQuery instance?

Edit:

<Field RefName='Project'/>

to

<FieldRef Name='Project'/>