Of course you can do that:
1) Create Servlet classes / JSP files. Package them all in a jar file. Don't include web.xml or any other files.
2) Import the jar in your web application classpath.
3) Configure Servlet classes and JSP files in your web.xml as below:
For JSP:
<servlet>
    <servlet-name>MyJSPFile</servlet-name>
    <jsp-file>/path/to/jsp/MyJSP.jsp</jsp-file>
</servlet>
<servlet-mapping>
    <servlet-name>MyJSPFile</servlet-name>
    <url-pattern>/MyJSP.jsp</url-pattern>
</servlet-mapping>
For Servlet:
<servlet>
    <servlet-name>MyServlet</servlet-name>
    <servlet-class>my.servlet.classpath.MyServlet</servlet-class>
</servlet>
<servlet-mapping>
    <servlet-name>MyServlet</servlet-name>
    <url-pattern>/MyServlet.do</url-pattern>
</servlet-mapping>