To make a layer transparent, you can use the Opacity and Merge mode settings, but these work on the entire layer. You can also make only certain parts of a layer transparent, which gives you more artistic control.
The easiest way to create transparent areas in a layer is to use a transparent gradient. The transparent parts of the gradient will create transparent areas in the layer. If you make all the other layers invisible, a pattern of blocks will show the transparent areas.
Another way of creating transparent areas is to use the Solid Color setting of transformations and coloring algorithms. Solid colors with an opacity value of less than 255 create transparent areas. Many transformations, such as Clipping in Standard.uxf, use this to create masking effects.
The Transparent icon before the layer toggles transparent areas on and off. Use it to quickly verify the transparent areas and to see what difference they make to the final image.