maf-cut cuts out parts of MAF format alignments. For example:
maf-cut chr7:1234000-1235000 alignments.maf
This gets alignment parts within the range 1234000-1235000 of the sequence named "chr7".
The ranges are zero-based. For example, chr7:0-1000 means the first 1000 bases of chr7.
You can omit the sequence name:
maf-cut 1234000-1235000 alignments.maf
Then, the range applies to the topmost sequence in each alignment.