The most common and most likely answer to this crossword clue is the 6 letter word IODINE
I've seen this crossword clue in The Guardian
I
O
D
I
N
E
More clues leading to the result IODINE
Buddy explains!

The straight part
We know that "What’s applied during period in ER" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case what’s applied during period in er = iodine.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 IODINE mean?
IODINE noun- A chemical element (symbol: I) with an atomic number of 53; one of the halogens.
- An antiseptic incorporating the element.
- An iodide.
- To treat with iodine.