MyBuild.fsx

#r "Microsoft.Build"
#r "Microsoft.Build.Framework"
#r "Microsoft.Build.Engine"

open System
open Microsoft.Build.BuildEngine
open Microsoft.Build.Framework

let engine = new Engine()
engine.RegisterLogger(new ConsoleLogger())
let project = new Project(engine)
project.Load("MyProjectFile.proj")
let succeeded = engine.BuildProject(project, "Main")

MyProjectFile.proj

<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="4.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
  <Target Name="Before" BeforeTargets="Main">
    <Message Importance="High" Text="Running Before" />
  </Target>
  <Target Name="Main">
    <Message Importance="High" Text="Running Main" />
  </Target>
</Project>