平滑滚动到树中的所需位置

$(function () {
    $('.tree li:has(ul)').addClass('parent_li').find(' > span').attr('title', 'Collapse this branch');
    $('.tree li.parent_li > span').on('click', function (e) {
        var children = $(this).parent('li.parent_li').find(' > ul > li');
        if (children.is(":visible")) {
            children.hide('fast');
            $(this).attr('title', 'Expand this branch').find(' > i').addClass('icon-plus-sign').removeClass('icon-minus-sign');
        } else {
            children.show('fast');
            $(this).attr('title', 'Collapse this branch').find(' > i').addClass('icon-minus-sign').removeClass('icon-plus-sign');
        }
        e.stopPropagation();
    });
});

$('#search').on('keyup', function (e){
  if(e.which == 13) { // тут проверка на нажатие клавиши "Enter" чтобы скрол не срабатывал при каждом нажатии клавиши   
    var val = $(this).val().toLowerCase()
    if (val) {
      $('ul li span').each(function(idx, obj){
        if ($(obj).text().toLowerCase().indexOf(val) !== -1){
          $(obj).addClass('highlight')
          //тут чуток напутал в предыдущем ответе
          this.scrollIntoView({ behavior: 'smooth' })
        }else{
          $(obj).removeClass('highlight')
        }
      })
    }
    else
      $('ul li span').removeClass('highlight')
  }
})

.tree {
    min-height:20px;
    padding:19px;
    margin-bottom:20px;
    background-color:#fbfbfb;
    border:1px solid #999;
    -webkit-border-radius:4px;
    -moz-border-radius:4px;
    border-radius:4px;
    -webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.05);
    -moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.05);
    box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.05)
}
.tree li {
    list-style-type:none;
    margin:0;
    padding:10px 5px 0 5px;
    position:relative
}
.tree li::before, .tree li::after {
    content:'';
    left:-20px;
    position:absolute;
    right:auto
}
.tree li::before {
    border-left:1px solid #999;
    bottom:50px;
    height:100%;
    top:0;
    width:1px
}
.tree li::after {
    border-top:1px solid #999;
    height:20px;
    top:25px;
    width:25px
}
.tree li span {
    -moz-border-radius:5px;
    -webkit-border-radius:5px;
    border:1px solid #999;
    border-radius:5px;
    display:inline-block;
    padding:3px 8px;
    text-decoration:none
}
.tree li.parent_li>span {
    cursor:pointer
}
.tree>ul>li::before, .tree>ul>li::after {
    border:0
}
.tree li:last-child::before {
    height:30px
}
.tree li.parent_li>span:hover, .tree li.parent_li>span:hover+ul li span {
    background:#eee;
    border:1px solid #94a0b4;
    color:#000
}
 .highlight {
    background: red;
  }

<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/js/bootstrap.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.2.2/jquery.min.js"></script>
<link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.0.0/css/bootstrap.css" rel="stylesheet"/>
<link href="https://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.1/css/bootstrap-combined.min.css" rel="stylesheet"/>
<input title="search" name="Name" id="search" type="text" placeholder="search">
<div class="tree well">
    <ul>
        <li>
            <span><i class="icon-folder-open"></i> Theme</span> <a href="">href</a>
            <ul>
                <li>
                	<span><i class="icon-minus-sign"></i> Standard</span> <a href=""></a>
                    <ul>
                        <li>
	                        <span><i class="icon-leaf"></i> Grand Child</span> <a href="">href</a>
                        </li>
                    </ul>
                </li>
                <li>
                	<span><i class="icon-minus-sign"></i> Child</span> <a href=""></a>
                    <ul>
                        <li>
	                        <span><i class="icon-leaf"></i> Grand Child</span> <a href=""></a>
                        </li>
                        <li>
                        	<span><i class="icon-minus-sign"></i> Grand Child150</span> <a href="">href
                                <li>
	                                <span><i class="icon-minus-sign"></i> Great Grand Child</span> <a href=""></a>
		                            <ul>
		                                <li>
			                                <span><i class="icon-leaf"></i> Great great Grand Child</span> <a href=""></a>
		                                </li>
		                                <li>
			                                <span><i class="icon-leaf"></i> Great great Grand Child</span> <a href=""></a>
		                                </li>
		                             </ul>
                                </li>
                                <li>
	                                <span><i class="icon-leaf"></i> Great Grand Child</span> <a href=""></a>
                                </li>
                                <li>
	                                <span><i class="icon-leaf"></i> Great Grand Child</span> <a href=""></a>
                                </li>
                            </ul>
                        </li>
                        <li>
	                        <span><i class="icon-leaf"></i> Grand Child</span> <a href=""></a>
                        </li>
                    </ul>
                </li>
            </ul>
        </li>
        <li>
            <span><i class="icon-folder-open"></i> Parent2</span> <a href=""></a>
            <ul>
                <li>
                	<span><i class="icon-leaf"></i> Child</span> <a href=""></a>
		        </li>
		    </ul>
        </li>
    </ul>
</div>

$("a").click(function(event) {
  event.preventDefault();
  $('html, body').stop().animate({
    scrollTop: $('#b1').offset().top
  }, 600, 'linear');
});

#b1 {
  wight: 200px;
  height: 400px;
  background-color: red;
}

#b2 {
  wight: 200px;
  height: 400px;
  background-color: green;
  position: relative;
}

#b2>a {
  position: absolute;
  bottom: 50px;
}

<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
<div id="b1">Блок1</div>
<div id="b2">Блок2
  <a href="">нажми</a>
</div>