How do I use alias in where clause?

You can't directly do this...but you can wrap an additional select around it all and use the where clause:

    select * from 
   (   SELECT
   Trade.TradeId, 
   Isnull(Securities.SecurityType,'Other') SecurityType, 
   TableName,
   CASE 
   WHEN 
   SecurityTrade.SecurityId IS NOT NULL  
   THEN 
   SecurityTrade.SecurityId
   ELSE 
   Trade.SecurityId
   END AS PricingSecurityID,
   sum(Trade.Quantity)OVER(Partition by Securities.SecurityType,       SecurityTrade.SecurityId,Trade.Price, Buy,Long ) as sumQuantity,
    --added porfolio id for Getsumofqantity
    Trade.PortfolioId,
     Trade.Price,
     case
     when (Buy = 1 and Long = 1) then 1
     when (Buy = 0 and Long = 0) then 1
     else 0
    end Position
    from
    Fireball_Reporting..Trade
    where porfolioid =5 and Position =1 
    )x
    where x.position = 1

You can't, not directly.

If you wrap the whole query in a sub-query, however, it works fine.

SELECT
  *
FROM
(
  SELECT
    Trade.TradeId, 
    Isnull(Securities.SecurityType,'Other') SecurityType, 
    TableName,
    CASE 
      WHEN SecurityTrade.SecurityId IS NOT NULL THEN SecurityTrade.SecurityId
                                                ELSE Trade.SecurityId
    END AS PricingSecurityID,
    sum(Trade.Quantity)OVER(Partition by Securities.SecurityType,
    SecurityTrade.SecurityId,Trade.Price, Buy,Long ) as sumQuantity,
    --added porfolio id for Getsumofqantity
    Trade.PortfolioId,
    Trade.Price,
    case
      when (Buy = 1 and Long = 1) then 1
      when (Buy = 0 and Long = 0) then 1
                                  else 0
    end Position
  from
    Fireball_Reporting..Trade
  where
    porfolioid = 5
)
  AS data
WHERE
  Position = 1   

This means that you don't need to repeat the CASE statement in WHERE clause. (Maintainable and DRY).

It is also a structure that allows the optimiser to behave as if you had simply repeated yourself in the WHERE clause.

It's also very portable to other RDBMSs.

In SQL Server, then you also have another option...

SELECT
  Trade.TradeId, 
  Isnull(Securities.SecurityType,'Other') SecurityType, 
  TableName,
  CASE 
    WHEN SecurityTrade.SecurityId IS NOT NULL THEN SecurityTrade.SecurityId
                                              ELSE Trade.SecurityId
  END AS PricingSecurityID,
  sum(Trade.Quantity)OVER(Partition by Securities.SecurityType,
  SecurityTrade.SecurityId,Trade.Price, Buy,Long ) as sumQuantity,
  --added porfolio id for Getsumofqantity
  Trade.PortfolioId,
  Trade.Price,
  position.val AS Position
from
  Fireball_Reporting..Trade
CROSS APPLY
(
  SELECT
    case
      when (Buy = 1 and Long = 1) then 1
      when (Buy = 0 and Long = 0) then 1
                                  else 0
    end AS val
)
  AS position
where
  porfolioid = 5
  AND position.val = 1

The SQL-Server docs says:

column_alias can be used in an ORDER BY clause, but it cannot be used in a WHERE, GROUP BY, or HAVING clause.

Similar in the MySQL doc it says:

Standard SQL disallows references to column aliases in a WHERE clause. This restriction is imposed because when the WHERE clause is evaluated, the column value may not yet have been determined.

In MySQL you can at least reuse aliases in the SELECT clause