CloneCD creates .CCD files, which are just a bit different than ISOs. Most VirtualCD programs will mount them just like ISOs, though, and if you've got CloneCD 4, you can just mount them with Virtual CloneDrive.
To create a .CCD image in CloneCD 4: click on "Read to Image File", choose the drive with the CD in it, choose the appropriate CD type, browse to the path where you want the image file (you can also create a Cue Sheet, which allows most other programs to use .CCD files easily), hit OK, and it starts reading the image.