What you are looking for is PHP’s modulo operator and adjust markup as necessary:
<?php
$i = 0;
$did_hr = false;
$post_args = array( 'post_type' => 'Student Form', 'posts_per_page' => 6 );
$post_query = new WP_Query( $post_args );
if ( $post_query->have_posts() ) :
while ( $post_query->have_posts() ) : $post_query->the_post(); ?>
<?php if ( $i % 3 == 0 ) : ?>
<section class="main_section" id="masc">
<div class="container cardbox_1">
<div class="row cardbox_horizontal d-flex justify-content-center">
<?php endif; ?>
<!-- while loop -->
<div class=" col-md-4 cards">
<div class="card card_1">
<h3 class="h3 card_head text-uppercase">
<?php the_title(); ?>
</h3>
<div class="center_image d-flex justify-content-center">
<a rel="external" href="https://wordpress.stackexchange.com/questions/356985/<?php the_permalink()?>">
<img class="image_head" src="<?php echo get_the_post_thumbnail_url(); ?>" alt="">
</a>
</div>
<div class="para_head">
<?php the_content(); ?>
</div>
<div class=" d-flex justify-content-end">
<a href="#" class="btn btn-primary">VIEW MORE</a>
</div>
</div>
</div>
<?php $i++; if ( $i != 0 && $i % 3 == 0 ) : ?>
</div>
</div>
</section>
<?php if ( ! $did_hr ) : $did_hr = true; ?>
<!-- middle section-(should not loop -this considered a border to top and bottom sections)ending -->
<section id="babg">
<div class="container">
<div class="row ">
<div class="col-md-12">
<hr class="this bbg">
</div>
</div>
</div>
</section>
<?php endif; ?>
<!-- middle section ending -->
<?php endif; ?><!-- while loop-->
<?php endwhile; // ending while loop ?>
<?php else: ?>
<p><?php _e( 'Sorry, no Students matched your criteria.' ); ?></p>
<?php endif; // ending condition ?>