Start by opening the icon in the Icon Editor by clicking on the Edit icon button. Select the element that you want to make transparent.

Then, click the colour picker and click on the little box with a red cross. Click OK. 

This will make the selected element transparent. 

Read more about:
​How to change the color of icons using the Icon Editor
​How to work with fill and stroke color
​How to change the canvas color
​How to download an icon from the Icon Editor