After you import, any graphics in your FrameMaker files are put in the same folder as your converted FrameMaker files. This looks messy and probably isn't what you wanted. You can easily fix this.
In the Content Explorer, click the Show Files button
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After you click the Show Files button, a two-pane view opens. You can expand your folders or create a new folder by clicking the New Folder button
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On the right side, select one or more files you want to move. Drag them to the folder on the left where you want to store them. The Resources\Images folder is the default location for new images that you create in Flare, so you may want to drag all of your graphic files to that folder (you may need to manually create the "Images" subfolder first). All of the standard Windows multi-select options are available.
You are prompted to update links when the files are moved. Make sure you click Update so that Flare knows where these files have been moved to and how to find them.
For more information see Organizing Topics in the Content Explorer.