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Try:
sed -e :a -e 's/\(...\)[^*]/\1*/;ta' file
GNU sed:
sed ':a;s/\(...\)[^*]/\1*/;ta' file
--
Can it be perl?
perl -pe 's/(?<=...)./*/g' file

Trysed -E 's/(...)./\1*/; :A s/
[^*]/**/; tA' file2
aba*****
cdc*******
efe******

For legibility I've used the -E (= -r) option so the parentheses etc. don't need to be escaped.

Those commands are trying to load the entire line into memory at once, which won't work on a 64 32-bit system since there's a 4GB limit on per-process memory and sufficient clutter in the way that...