Hi Dora,
This is outside the scope of what the MplusAutomation package is specifically intended to accomplish. That said, I would take a look at list.files() and lapply() in base R, and rbindlist() and fread() in the data.table package. If you put those together, it's easy to read and combine large numbers of files. Something like this:
flist <- list.files(path=getwd())
res <- data.table::rbindlist(lapply(flist, data.table::fread))
Hope that helps,
Michael