I know that there is padding and margining feature to make my scene builder features to look prettier. But I was wondering how to make lines around features(e.g. buttons, gridpane, canvas, etc.) to separate from others and to make is look better.
Maybe look at css border style properties.:
E.g. http://www.java2s.com/Code/Java/JavaFX/UsingCSStostyletheborder.htm
You can add "-fx-border-color", "-fx-border-style" and "-fx-border-width" in the style section (under Properties) of your javafx nodes. W3Schools also has some good resources for CSS styling, so maybe check out https://www.w3schools.com/css/css_border.asp