are the positions saved in an image stack?
If so, you could use "Fiji" to separate them into single files.
The manual way would be:
Open the stack with Fiji
Goto "Image" > "Stacks" > "Stack to Images"
Save each image.
(Saving as .lsm will not be easy (impossible with fiji?). You could use the OME-TIFF format to save your images with meta data. If you really need the LSM format, there would be the possiblity to write a utility as this format is just a modification of the TIFF format but this would be a lot of work.
Of course it is possible to have the steps done automatically with a little script. Let me know, if you need help to create such a script.