The most common and most likely answer to this crossword clue is the 6 letter word GLAZED
I've seen this crossword clue in The Guardian
G
L
A
Z
E
D
More clues leading to the result GLAZED
Buddy explains!

The straight part
We know that "Put window in" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case put window in = glazed.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does GLAZED mean?
GLAZED verb- To install windows.
- To apply a thin, transparent layer of coating.
- To become glazed or glassy.
- For eyes to take on an uninterested appearance.
- A glazed donut, one with a coating such as sugar or chocolate.
- Of eyes: showing no liveliness.