The page you refer to is a good start to get familiar with processing NGS data, but there are (a lot more!!) functions in the BioInformatics toolbox that will help you with preprocessing. Now to your specific questions:
(1) how to filter (or mask) reads shorter than 10 nucleotides:
You can use the 'seqfilter' function ( over here) and then using something like the following:
your_filtered_data = seqfilter(yourdata.fastq, 'Method','MinLength','Threshold',10)
(2) how to treat paired-end reads
You are in luck, as there exist this thingy called 'seqsplitpe', which allows you to split merged paired-end sequences into separate files (if that is something you want).
(3) how can I filter reads that have more than two N nucleotides
This is probably a combination of (a) importing your sequences and then (b) searching your sequences for your specific repeat of >N nucleotides. I believe there are no pre-fabricated functions in MATLAB for this, but there are numerous functions which allow you to analyze sequences in the Bioinformatics Toolbox.