You may create a copy of the default Vancouver style in Endnote and modify it as you preferred (e.g.: make it superscripted and not bracketed).
Below are the steps to do so:
Open Endnote, choose " Tools" from the top bar menu > Output Styles > Edit "Vancouver (For Endnote X9 or earlier : Choose "Edit" from the top bar menu > Output Styles > Edit "Vancouver")
Edit the template according to your preference.
(e.g. making it superscripted, deleting the bracket)
i) Choose " Templates" under Citations
ii) Highlight " Bibliography Number" in the field " Citation"
iii) Click the icon for superscript
iv) Delete the brackets (See the attached image)
Choose " Save As" under " File" from the top bar menu and save the revised style as " Vancouver superscript".
In your MS Word file, open the Endnote tab.
Select " Select Another Style…" from the Style pull-down menu.
Choose the newly created style " Vancouver superscript" form the list and click " OK".
Insert the reference from your Endnote library to your Word file using this new style.
You will find the in-text citation superscripted and not bracketed.