The first naming option is called Do not merge, single output for each input; output named as input. Choose this option if you do not wish to merge input files, just to keep the input file names and use them directly as output file names. This means if you have single page TIFF files, the output will be single page PDF files. If an input image has multiple pages, a multipage PDF file will be created out of it, but there will always be strictly one output PDF created for every single input image. This option is not used that often as the two others. Please see Figure 2 for an example.

Figure 2. Naming output files the way as the input files are named, no merging.

A: Input directory tree; B: Output directory tree