The transform layer option allows you to transform whole layers. You can shift, rotate, scale and mirror your selection or even whole layers. The checkboxes at the bottom allow you to further adjust the type of transformation:

• Transform all active layers:
  This checkbox is activated by default and encertains that your transformations are applied to all layers currently activated in your layer stack up. Deactivating it enlarges the transformation dialog with an additional layer stack up overview you can choose the layers from which you want your transformation applied to.
• Transform only selected objects:
  Activating this option causes only the objects you selected on their respective layers to be shifted.
• Auto adjust
  There are cases, especially when using a combination of different data formats like Gerber for your copper layers and Excellon for your drill layers, where you get an unwanted offset between your data sets. The auto adjust option is intended for these cases. You simply have to set a reference point in each layer you want to synchronise by clicking into the visualisation PCB-Investigator will then align your layers using the given points. For the sake of simplicity, it is recommended that you use small concise objects you can easily identify and mark on all needed layers.