Is it wise to use RepeatMasker on prokaryotes?
If I understood correctly your question, you want to mask those regions in a (FASTA?) genome. I think you could identify those regions using mummer and mask them using bedtools.
# align genome against itself
nucmer --maxmatch --nosimplify genome.fasta genome.fasta

# select repeats and convert the corrdinates to bed format
show-coords -r -T -H out.delta | awk '{if ($1 != $3 &amp;&amp; $2 != $4) print $0}' | awk '{print $8"\t"$1"\t"$2}' &gt; repeats.bed

# mask those bases with bedtools
bedtools maskfasta -fi genome.fasta -bed repeats.bed -fo masked.fasta

Have a look at nucmer and bedtools maskfasta options to fine-tune your analysis.