Lines, polygons and models in Altus all have the ability to be transparent, with the degree of transparency or opacity set with the alpha channel. There is also a way to set the transparency of a whole map layer.
To make a single polygon transparent you can set the alpha color value to something less than 255:
var colors3 = [new AltusUnified.Color(100, 200, 80, 99), new AltusUnified.Color(10, 100, 80, 99), new AltusUnified.Color(10, 100, 100, 99)];
var polygonStyle = new AltusUnified.PolygonStyle(colors3, colors3, 8, colors3, 2);
The value 99 is the alpha value. 0 is completely transparent (invisible). 255 is completely opaque.