Is there any way to get only parent terms from custom taxonomy or category?
Yes, just pass in the parent parameter to get_terms
when you call it, as Michael pointed out.
Since WP 4.5 this is the recommend usage:
$myterms = get_terms( array( 'taxonomy' => 'taxonomy_name', 'parent' => 0 ) );
Prior to WP 4.5 this was the default usage:
$myterms = get_terms( 'taxonomy_name_here', array( 'parent' => 0 ) );
Will return all terms that have a parent value of 0
, ie. top level terms.