There are two modes for file merge to assist users having better control of files in the merged destinations. The two modes are:
This first example shows you the settings and the results of Structure Mode in File Merge. Two ways to keep merged files:
Here, suppose your source folder is "03-2005" with sub-folders "my1", "my2", "my3", etc. as shown in the picture.

Your target folder will keep the original file structure as shown in picture below where all sub-folders are kept to hold individual files in their original place.

Your target folder will keep all files in one folder in alphabetical order.
Now, we are looking at the settings and the results of Overwrite Modes in File Merge. Two different settings can be selected from:
The resulting folder of this setting looks the same as the original files because the old files with the same names have been replaced by the files of same name but with newer dates.
The result of this setting can be seen as the changed file names are similar to that of different versions of a same file. This is so designed to make your tracking of the files easier.