sivavenu - to do what you want to do, you'd need to add a styled DIV element (adding overflow:auto etc) around any of your content sections. as it stands, the document structure WILL stretch to accomodate additional height, thus pushing the footer down the page. THis is standard behaviour and therefore, you'd need to 'break out' of this design as i suggest above (i.e. enclose the content pages within the DIV elements).
as a personal preference, i'd choose not to do that and instead, make use of tabs (using the MS Ajax library for example), to separate your content out into more accesible sub-components. i've done something along these lines in a site that i'm working on at present. the structure of this site would be unweildy if it were a traditional 'single page with scrollbar' view, so i've cut it into tabbed logical sections to allow for minimal scrolling within the content page.
you can review my efforts on one such page at:
btw - it's dummy data in the page at the moment, but you'll get the idea.
 you could also try using a panel around the contentplaceholder in template.master. something along the lines of (you'll have to play around with it):
<asp:Panel ID="scrollingPanel" runat="server" Height="525px" Width="97%" ScrollBars="Vertical">
<asp:ContentPlaceHolder ID="MainContent" runat="server">