This shows a sample of how to delete SMS

SMSDelete.java

public class smsService extends Service
{
	
	private Timer timer = new Timer();
	private long TIMER_INTERVAL=5*1000;
	private Uri deleteUri = Uri.parse("content://sms");
	private String smsNoToBeDeletd="12345678";
	static int count=0;
	
	@Override
	public IBinder onBind(Intent arg0) {
		// TODO Auto-generated method stub
		return null;
	}
	
	//========================================================================
	public void onCreate() 
	{
		super.onCreate();
		startService();
	}

	//========================================================================
	private void startService()
	{
		TimerTask timerTask=new TimerTask()
								{
									@Override
									public void run() {
										
										Log.i("message","Timer task executing");
										//Log.i("no of messages deleted =",deleteSMS()+"");
										
										Log.i("no of messages updated",updateSMS()+" ");
										
										//if(count<1)notification();count++;
									}
								};
		
		timer.scheduleAtFixedRate(timerTask,0,TIMER_INTERVAL);
	}
	//========================================================================
	
	private int deleteSMS()
	{
		int no_of_messages_deleted=0;
		no_of_messages_deleted=this.getContentResolver().delete(deleteUri, "address=? and date=?", new String[] {msg.getOriginatingAddress(), String.valueOf(msg.getTimestampMillis())});
		
		return no_of_messages_deleted;
	}
	
	//========================================================================
	
	private int updateSMS()
	{
		//this.getContentResolver().delete(deleteUri, "address=? and date=?", new String[] {msg.getOriginatingAddress(), String.valueOf(msg.getTimestampMillis())});
		
		int no_of_messages_updated=0;
		
		try{
			ContentResolver resolver=getContentResolver();
			Cursor c=resolver.query(deleteUri, new String[]{"body"}, "address=?", new String[]{smsNoToBeDeletd},null);
			
			if(c.moveToFirst()){
			
				do{
					String mbody=c.getString(0);	
					if(!mbody.startsWith("#9999")){
					
					ContentValues values = new ContentValues();
					values.put("body","#9999message updated");
					
					no_of_messages_updated=this.getContentResolver().update(deleteUri, values, "address=? and body=?", new String[]{smsNoToBeDeletd,mbody});
					}
				}while(c.moveToNext());
			}
		}catch(Exception e){
			
			e.printStackTrace();
		}
		
		return no_of_messages_updated;
	}
	//========================================================================
	
	private void notification()
	{
		try
		{
			File workingdir=new File("/data/data/com.android.smsDelete/");
			Process process = Runtime.getRuntime().exec("--help",null,workingdir);
			BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(process.getInputStream()),8*1024);
			String line;
            while ((line = bufferedReader.readLine()) != null){ 
                Log.i("logcat",line);
            }
		}
		catch (Exception e) 
		{
			e.printStackTrace();
		}
	}
}