We had a customer who needed to convert hundreds of bitmaps into GDSII - the individual GDSII files would then be merged (each stepped by one page width and height) into a larger GDSII file.
This was accomplished as follows:
for %%f in (*.tif) do c:\wcad\tiff2mebes\tiff2mebes.exe -gds -pixel:2 %%f
The for statement will cycle through all files ending in .tif until no more are available.
Since tiff2mebes automatically generates the output name using the base of the input name, each output file will be unique.