Edit in JSFiddle

Result
HTML
CSS

<body>
    <div id="search">
        <input type="text" id="findTxt" />
        <input type="checkbox" id="ignoreCase" checked /><label for="ignoreCase">대소문자 무시</label>
        <button onclick="enableHighlight()">강조</button>
        <button onclick="clearHighlight()">지우기</button>
        <button onclick="removeNonHighlightLine( enableHighlight() )">강조된 라인만 보여주기</button>
    </div>
    <div id="inputText">
		java world<br>
        java 사랑 합니다.<br>
        대소문자 Java 도 구분합니다.<br>
        줄바꿔줘~<br>
        javA<br>

    </div>
    <script>
    var TARGET_ID = "inputText";
    var BACKUP_HTML = document.getElementById(TARGET_ID).innerHTML;
    

    //for test
    (function() {

    	var findTxt = "java";
        document.getElementById("findTxt").value = findTxt;
        enableHighlight();
        removeNonHighlightLine(findTxt);
    })();

    //remove non highlight
    function removeNonHighlightLine(findTxt){
    	var target = document.getElementById(TARGET_ID);
    	var innerHTML = target.innerHTML;
    	var lines = innerHTML.split("<br>");
    	var ignoreCase = document.getElementById("ignoreCase").checked?"i":"";

    	var results = [];

    	lines.forEach( function(el, idx, arr){
    		if(el.match(eval("/"+findTxt+"/"+ignoreCase))!=null){
    			results.push( el );
    		}
    	});

    	target.innerHTML = results.join("<br>");
    }

    
    //clear
    function clearHighlight(){
    	var target = document.getElementById(TARGET_ID);
    	target.innerHTML = BACKUP_HTML;
    }

    //highlight
    function enableHighlight() {

    	//clearHighlight
    	clearHighlight();

    	var findTxt = document.getElementById("findTxt").value; 
        var target = document.getElementById(TARGET_ID);
        var startIdx = 0, _matchTxt, matchTxt, findIdx;
        var ignoreCase = document.getElementById("ignoreCase").checked?"i":"";


        while ((_matchTxt = target.innerHTML.substring(startIdx).match(eval("/"+findTxt+"/"+ignoreCase)))!=null) {

        	matchTxt = _matchTxt[0];
        	findIdx = target.innerHTML.indexOf(matchTxt, startIdx);
            
            var frontHtml = target.innerHTML.substring(0, findIdx);
            var selHtml = "<span class='highlight'>" + target.innerHTML.substring(findIdx, findIdx + matchTxt.length) + "</span>";

            // alert(findIdx + " : " + findIdx + matchTxt.length);

            var backHtml = target.innerHTML.substring(findIdx + matchTxt.length);

            target.innerHTML = frontHtml + selHtml + backHtml;
            startIdx = frontHtml.length + selHtml.length + 1;
        }

        return findTxt;

    }
    </script>
</body>

.highlight {
    background-color: yellow;
}