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There is a chance that the submitter's submitted the samples concatenated into just two files. In that case the fastq headers may contain the sample names that could be used to split the samples up. What SRA# are you looking at?
You can search ENA with the accession number you have to see if they have more than 2 fastq files available. You can download fastq files directly from ENA.
I have checked ENA database there are only 2 files with names file1 and file2. I was also thinking that the documents are submitted into 2 files. Is there any way I can separate them OR how to process these files if I have to use them as such? Thanks
Just like genomax already asked you: please add the SRA number so we can have a look.