Maps containing data frames that overlap other data frames or graphics elements are displayed in ArcMap Layout view as transparent. However, when they are printed or exported, the top data frame background is opaque white, obscuring the layer below.
Each individual data frame or graphic object is processed separately. If the data frame or graphic element contains raster data, transparency, or picture symbology, it becomes rasterized. 'No data' or hollow fill areas, which look transparent in ArcMap layout, print or export as white, filling the entire background of the data frame or graphic element.
The apparent no data/hollow fill on output is not supported. The limitation of transparent graphics and transparent data frames containing rasters are limitations of the Microsoft graphics engine (GDI) implemented in ArcGIS Desktop.
It is highly recommended to use ArcGIS Pro for printing and exporting, especially when experiencing issues caused by the limitations of the ArcMap display engine. More specifically, ArcGIS Pro is not restricted by the graphical device interface (GDI) limitations that some users experience in ArcMap. For example, transparency is natively supported in ArcGIS Pro, preventing the rasterization of layers. Additionally, ArcGIS Pro supports transparency in layout elements.
Note: ArcGIS Pro does not support exporting Adobe Illustrator files; it is recommended to export using PDF or SVG instead. Also, because ArcGIS Pro does not use the Windows GDI, font substitution or fallback does not occur in ArcGIS Pro. Boxes may appear if using characters unsupported by the chosen font.
Since this is a known limitation in ArcMap, there is no way to preserve transparency between data frames with rasterized elements using ArcMap. The workarounds below concern either removing the rasterization, or modifying the layout to avoid obscuring other layers.
Note: In ArcGIS 9.2, use the 'vectorize layers with bitmap markers/fills' option, under the Format tab in the export dialog box, to prevent bitmap markers or fills from causing rasterization.