You set the transparency in your paint program. What paint program are you using? Usually you will have a background layer that is fully transparent. You then add details in other layers. As each layer can have it's own transparency you can build up your image. For example, if you want to make the windows on the right in your image half transparent you would set the layer to be 50% transparent in your paint program and then export that as a PNG.
When you export the image from your paint program it is also important to ensure that the paint program is exporting in the PNG with transparency format.
Once you have your texture with transparency you can use the material editor in 3DS or Blender to set how the transparency is processed.
Opaque is no transparency
Mask is either opaque or transparent based on the alpha channel.
Blend is transparency is based on the alpha channel.
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