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That works fine for the sample, but there would not be lazy matching, so if the pattern would appear twice on a line, this would not work for text between multiple patterns on the same line.

An...

You were very close, .* is greedy and will match the longest string it can.

You need this:

$ sed -e 's/\[\[.\{2,3\}:[^]]*\]\]//g' sed1.txt
1 [[special:linguagem]] FISICA
2 PORTUGUES
3 ...