If you're scanning many images in one session, the most efficient way to do this is to scan each image once and save the raw CCD data in a file. Once the raw CCD data is stored in a file, you can re-process the scans in a variety of ways without needing to re-insert the image into the scanner. This minimizes the opportunities for the film to get dusty, minimizes film handling, and is the fastest way to re-process all the scans if you decide you want to use different options for the scans.
To do batch scanning, you first need to set up the options in the "Input" tab for the scanner and media type you're using. First, set "Input|More options" and use "File|Default options" to set up default options. Then set "Crop|Preview area" to "Default", set "Crop|Crop size" to "Maximum", set "Crop|Y images" to 1, and in the "Output" tab un-check all the options except for "Output|Output raw file" (which should be on).
When you scan each image, files named scan0001.tif, scan0002.tif, etc. will be created. You can also change the folder and file names by changing the "Output|Raw file name" option. To re-process these raw files, set the "Input|Scan from" option to "File", set "Input|Scan from file" to point to the starting file in the series (normally scan0001.tif), set "Input|Scan mode" to the type of scanner that the files came from, use the "File|Default options" command to set all the other options to their default values, then set up the other options as if you were scanning from the scanner instead of a file.
Set "Input|Batch scan" to "All" to scan all files, or set it to "List" and manually set the frame numbers. For instance, if you set this to "1-3,5,7", then scan0001.tif, scan0002.tif, scan0003.tif, scan0005.tif and scan0007.tif will be processed when you press the "Scan" button.
You may also want to follow the procedure in the "Advanced Workflow Suggestions" section of this User's Guide for locking the exposure and film base color for the whole roll of film. This will result in scans that will have the best quality.